If I had to guess I would imagine Checkpoints are a way to tutorialize the mod without writing paragraphs explaining everything. For that it is a great feature but later down the tech tree it starts to get quite annoying. For example I'm working my way towards train and therefore, Traffic Control. But on the way there I've ran into several checkpoints a few of which seem to be mostly just an annoyance. Mass production demonstration, Gravel disposal, Freight transport demonstration and freight logistics demonstration in particular feel unnecessary.

I get that other player's might find it useful to walk them through the tech tree but would it be possible to make checkpoints in general optional?

Gravel disposal is in no way optional. What's the alternative, keep building more warehouses? If you put it off too long after the tech for dealing with it, you may forget that it even exists and when your gravel warehouses start to get too big you'll think there's no solution.

How do you propose to make use of traffic control without trains, and if you have trains, why are checkpoints for them such a problem?

Checkpoints are not purely for a tutorial. They also just make sense. How do you research things that improve on existing technologies if you've never once even used the basic technologies? You need to actually have a train to learn to build train stations. You have to actually automate train travel between 2 stations before you learn to manage traffic for multiple trains travelling between multiple stations. These are iterative refinements of your technology after you experiment with the earlier stages of the technology. Why should you have the knowledge to be able to leap frog directly to the most advanced versions of a technology that you haven't made use of at all yet?

Gravel disposal also has a secondary purpose that may not be so obvious. Until you get calcium chloride in electrical engineering, mineral dust is the best way to void chlorine. Early on in mechanical engineering, chlorine is manageable without this. But by the end when you get aluminum, you start to need a lot of caustic, and generally at this point begin to have a surplus of chlorine. None of this is particularly obvious, so dealing with the gravel checkpoint nudges you toward this solution that you're about to need for chlorine.

If you're planning to go big with a train base, then perhaps you need more gravel than average for rails, so maybe that will be a big enough sink for gravel for now (though probably not indefinitely). However, that still leaves chlorine without a sink. The checkpoint is actually for using mineral dust and hydrochloric acid. If you're using the gravel for now, that dust doesn't actually have to come from gravel. Most people have more than enough gravel already at that point, but if you don't and need more to void chlorine, you can create extra mineral dust intentionally, for example with limestone.

So there are two problems:
First, I'm an experienced player so I don't need much in the way of tutorials. So I am able to set my own goals effectively I don't need hand holding. So it's only getting in my way. For example, I just got purple science semi-automated just so I can rush through to trains as it will let me modularize my base. But before I can use trains properly I have to generate a handful of canisters, a small rail loop and a train to burn the fuel. If I don't do that then I can't even start the research for train stations. I don't think I have to explain how that's a huge waste of time. I could have been researching in parallel to my automating setup but instead of I have to do this weird manual step first.

Second, The checkpoints are sometimes not even related to the thing they gate. The gravel disposal is perfect example I am in no way in trouble of running out of storage or having trouble disposing it. I can use it for landfill, dispose of it if I really need to, or use it for the billion train tracks I want to create. Another example is cars being blocked by lubricant yet you don't need it to make the car. So I could have had the car hours ago but I don't because it's arbitrarily blocked. Then using the first grade fuel blocks train stops and methanol fuel yet most players I doubt will even use trains until they have train stops at least and usually not til signals.

So while they are good in theory they come with all these annoying side effects that just get in my way instead of actually helping.

Also I just noticed the problem is even worse. Rail signals requires lubricant, cars, red belts, and a bunch of those dependencies for absolutely no reason. I guess this problem goes deeper than just checkpoints...

I just reached my breaking point with the checkpoints.
The early ones, despite feeling bad, atleast made sense.
Melting Iron ore is stuff youd do anyway.
But now i had 2 backtoback that straw'ed it.

1. Fuel and Trains.
   My base is about as big as the zoomed out screen with lots of empty space still to fill.
   Ive only used a fraction of the starting patches.
   Im hours away from using Trains to get new Ore in yet i just spend 2 minutes driving in a circle for a checkmark.

2. Plumbing.
   Build 10 Pumps. Easy, i have those anyway.
   Build 6 Relieve Valves. Easy, i have those anyway.
   Build 10 MediumTank2. Fuck no.

Im using 15 level 1 tanks around my base which are more than enough.
The level 2 are ridiculously expensive for only twice the storage i dont need.

While i dont have the programming skills to remove the checkpoints from the game
a bit of wildcard-replace and now all of them check for a handful of iron ingots.
Maybe this will cause errors later but for now it lets me play factorio instead of feeling like
im being strung along on a curated adventure.

agreed
checkpoints are great in the beginning because everything's so different, but at some point you just have to accept that someone who is playing this mod has played Factorio before.
I have tons of random warts in my factory for the sole purpose of satisfying some checkpoint that I'll never make use of, for a base I will eventually demolish because you're obviously supposed to use logistics bots for everything

agreed
checkpoints are great in the beginning because everything's so different, but at some point you just have to accept that someone who is playing this mod has played Factorio before.
I have tons of random warts in my factory for the sole purpose of satisfying some checkpoint that I'll never make use of, for a base I will eventually demolish because you're obviously supposed to use logistics bots for everything.
It feels less like I'm playing factorio and more like I'm just doing stuff because someone said so.
There is supposed to be fun in picking and choosing what techniques you think are necessary and which one's aren't, but for some reason the mod insists I unlock everything

For what it's worth, I really like the checkpoints and with the base game had them too! But I also don't see why some of them (the non-victory-related ones) couldnt be disabled in the mod options.

I don't think the checkpoints get in the way too much, at least in the early game. They ask for small amounts of stuff which is easily produced with a temporary factory if you're not ready for mass production yet (I like to know a bit more about what I'm going to use something for before setting up mass production). For the ones which ask to build something, you can just place the required amount of buildings and then remove them.

Most of the checkpoints I've fulfilled rather naturally, but plumbing deployment is a bit of a stick in the mud. I get the idea of relief valves, but they require at least 75% pressure while the early pipes can only handle up to 60%. Because of that the valve has to be directly connected to a tank, and on the other side a pump must be directly connected as well. This combination is annoyingly unwieldy and I much prefer using a pump controlled by circuit network to move excess fluid out of the tank. I was able to make actual use of relief valves in a few places, but ended up forcing the checkpoint with useless buildings.

But thats one of the main problems.
A temporary setup for the sake of the checkpoint itself
is a nonsensical waste of time.
Id rather spend that time on removing the checkpoints from the mod itself.