Hmm, Cargo Ships may be impossible to be made fully compatible. The way each ship is programmed, you have the ship item in your inventory, and when you place it on the waterway, it creates two separate entities, the engine part (that you put fuel into) and the cargo part (which is the bulk of the entity).
When you mine it back up, only the cargo part of the entity gets saved, so all of the equipment placed into the engine part is simply deleted. So this basically removes the ability to put speed engines (since these do not affect cargo entities when placed into their equipment grids).
The only useful equipment that can be placed into a cargo wagon, is maybe personal roboports (and possibly the new inventory increase equipment, with space age), which I guess is fine, but a noteworthy limitation. Fluid wagon can't even use roboports because no inventory. The rest of the list just includes lasers, shields, batteries, and power generation. Oh, and I guess radar equipment, if you have that mod enabled.
The basic boat might be even worse off, since it can be placed as a car when placed off waterways, or as an engine/cargo duo, just like the bigger ships. If you place it as a car and pick it back, it retains the equipment inventory unless you place it down on a waterway. The inverse is also true; if you place it down on a waterway, it will retain its equipment inventory, until you place it in the open ocean. Either way is not good, and there's no simple way for me to prevent this from happening.
The safest thing I can really do is give the cargo part of the cargo and fluid ships an equipment grid, while preventing the basic boat and the engine parts from using equipment.
The new Aircraft mod worked perfectly with no other changes needed besides the name of the mod lol. Both added in v2.0.3
