It seems that pipes collide with independent boats from Cargo Ships. Though surprisingly not with ships on waterways.

Hum, gonna look into that

just revived from exileeeeee... was busy with studies, srry.
the boats that u drive are the ones that collide, but the big ones (used in the waterways) not, right?
I may see it later, as i'm still busy.

That's right. Ships and boats on waterways don't collide. Only the independent boats.

Well, made some shenanigans, but finally made it work.

At the end, it was because of the boats having weird collision_layers. Had to create my own layer and add all terrains, so now the pipes are placeable on any kind of liquid or semi-liquid (except of lava xd), as well as non-collidable with anything other than terrain itself.

the only downside is that, now the pipes overlap with anything, but this is something more deep than just editing a property... it's literally hard-coded into factorio, so i'm unable to change it. maybe on version 2.1

Well, it works for me. By anything you mean, any entity that is on the surface of the water? That's how it is supposed to be then.
There is only one (fixable) problem:
If another mod creates a new pipe, say "pipe-2" and sets pipe to be upgadable to pipe-2, then when you derive underwater pipe from pipe, you inherit its next_upgrade property. This causes factorio to refuse to load the mod, because underwater pipe has a next_upgrade target that has a different collision mask, which is not allowed. The solution here is to just delete next_upgrade property.

yep, any entity that is capable of "standing" on top of water is able to overlap with the pipes, both visually and physically.

and about the upgrade, i didn't think of that actually. i'm gonna check it and add the little patch (maybe it's also needed for my other mods)

done. plus also decided to bring something from "No Pipes Touching".

now all the scripts for the Runtime Stage aren't necessary: normal-underwater pipes won't be able to connect to ground ones, except for the underwater-underground pipe, which is the intended way.