Could you please put this into separate mods?
I really like to use some of those items but not use most of it.

For example I use the cokery and wood farm, but I don't care for the crushed stone (just use stone, it's fine...) or vanilla recipie changes (rails) at all.
I also don't want all the wood items (useless, really. Why do you want wood walls? by the time you're done building them, they're useless against medium biters), bio cannon (make it artillery ammo?), solar farm (just looks really out of place), etc.

I forked from your github but that seems to not be updated anymore. Plus removing stuff is a lot of work when those (unrelated) things should be separate modules in the first place. If you want to offer a package, just make an empty mod that has all the other modules as requirements. I believe it would be better if you let people pick and choose the smallest possible units.
It would also be more maintainable.

This feature creeping monolith is getting out of hand, imo.

Could you please put this into separate mods?
I really like to use some of those items but not use most of it.

Actually, the trend is going in the other direction. For the next major release, we've put the graphics, sounds etc. from Bio Industries (as well as parts of the Natural Evolution mods) in one external mod, so the mods containing the code will become much smaller.

For example I use the cokery and wood farm, but I don't care for the crushed stone (just use stone, it's fine...) or vanilla recipie changes (rails) at all.
I also don't want all the wood items

Would settings help, perhaps?

(useless, really. Why do you want wood walls? by the time you're done building them, they're useless against medium biters),

Some people advance their tech as fast as possible, others spend a lot of time in the burner stage. Wooden fences are immediately right from the start, while you have to research walls. If you have lots of trees in your starting area, you can just mine some trees and put up some cheap walls quickly. They won't stand a chance against bigger enemies, but if you put some dart turrets behind them (darts deal less damage than bullets, but dart turrets have a higher fire rate than gun turrets), they will keep small biters out at least. The best thing: Once you can afford to upgrade to stone walls, the resources are not wasted because you still can burn the wooden fences. :-)

bio cannon (make it artillery ammo?),

No. It's prototype artillery, it won't withstand the strain of real artillery shells! On the other hand, it's available much earlier (at least in the new version) than real artillery.

solar farm (just looks really out of place), etc.

Graphics have been reworked for the next version. Perhaps that will be better?

This feature creeping monolith is getting out of hand, imo.

Don't tell me -- I'm just putting the final touches on restructuring the things happening during the data stages. Separating everything was a walk through hell… But it's better organized now (or so I'd like to think), so it may be possible to make more things optional.

OK, I've added settings to turn off Wood products (bigger poles, bigger chests, wood pipes), Early wood based defenses (darts, dart rifle, dart turret, wooden fence), and Stone crushing (crushed stone will be replaced with stone in recipes). It's already possible to turn off the solar/power things (solar farm, solar plant+boiler, Musk floor, huge substation, and huge accumulator) and the Bio cannon. I'll add another setting to turn off the rail-related things (wooden rails, powered rails + connector, and wooden bridges).

Thank you.