The cargo aircraft can dock at a spidertron docking station, which means they can transfer 20 slots of cargo very quickly, and do not require any waterways to use so they're much easier to set up. Is this intended? They are quite a bit more expensive I suppose.

They aren't meant to replace ships, no, but they are very strong, possibly too strong. They can carry 20, which is a lot less than cargo ships' 100, and they can't carry containers.

They are intended to be used for things that you only need small amounts of, things that you need to deliver to lots of places (e.g. ammo) and things that can't be containerised (such as building materials, repair packs). Maybe I need to drastically increase the fuel consumption?

Oh if they can't carry filled containers then you can't really compare them to ships after all and they're fine. Containers are 10x more slot-efficient so it's 20 slots vs effectively 1000, and cargo aircraft sure aren't 50x faster. They're more like an alternative to long range delivery drones.

Yep exactly. You can manually load them with containers since there’s no easy way for mods to prevent this, but I’ve made it so that docks can’t be used to automatically load filled containers onto spidertrons and aircraft.

My thoughts about aircraft -
In my last playthrough I found that Cargo Aircrafts are pretty useful to bring uranium and titanium to base. You just need to get some purple+yellow tech first to get to aircrafts, then a lot of titanium to build them, and then yo can set routes to each resource patch on other islands slowly.
With cargo ships you usually have to wait until it's filled with 80 containers which takes forever (I mean specifically uranium/titanium, not common ores).
Generally you can think of aircraft as fast single container transport, they can hold 20 stacks which is exactly a container for all resources.
Process uranium/titanium in-place with electric smelters/centrifuges, after that there's so little finished product that one cargo aircraft is enough to bring it to base, and then it will even wait to be filled 80% of the time. The cost of a round trip is just a few rocket fuel, and you don't need to bother with containers, railroads or ship ports.
For waypoints, I made my aircrafts follow simple schedule -
1. go to home base unload dock, wait until cargo empty.
2. go 3-4 tiles away from unload dock, wait until fuel full, set logistic to fill it with exactly 100 rocket fuel (you should have logistic bots at this point already).
3. go to load dock on remote island, wait until specific item count (I use item count in case there's some mistake with inserting items, and for transferring both u-238 and u-235 at once)
So far, as I said, it's a lot more easier to set one airship per remote patch than make a whole ship infrastructure, but this is totally late game, I even put fusion reactor + exoskeletons on aircrafts to make then fly faster and use less fuel )

Also, combat aircraft is really the way to go, I always destroyed my base with hovercrafts in midgame and now I just fly over it ))

//edit: yeah, and I forgot something - it's 2 airships per each uranium/titanium patch. One to bring the resource, and another to bring barrels of acid/lube. Still neither of them needs any circuit logic, just simple 'wait until you're full with liquid or empty barrels' works, since barrels are not lost it's a closed loop.