[Aezeal]

that will make the idea of transport ships impossible to carry out unless it's all sailing and that will have limits on mapmaking since everything needs to be within one space square of something else.

On the other hand you could give regular commanders no amphibious option and make spaceships aquatic or amphibious. That would mean regular commander would need a magic item to cross space though (like they are not able to fly in the troop carriers.. a bit weird)
Also if you make the carriers amph and not aquatic that would then totally make land commanders obsolete since spaceships would be much more flexible.

If you make land commanders land only and ships water only you'd need another option to get the damn soldiers from their generals to the ships (and get the generals to cross space somehow) and do the same in reverse on the planet you want to invade... which seems difficult too.

PS I hope to have a workable space game up this hours.. I've only modded sporadically so could be that due to me [censored] up it'll not work the next year though.

Else you'll be able to fight ulm with ulm rebels (identical) on my ugly space map (which will be totally not polished just connections made in the editor (which sucks)