Very good point, and I'd suggest holding off for now. The controls are mostly locked down, but where it gets tricky is with ship customisation.
So in-game you can move your ship modules around and make it the way you want it, so that massive tower we have where you see all the lights representing damage to your ship? Only really works for that particular ship. So if in-game you've got your modules in a different place, that might throw a spanner in the works.
All the interactive buttons down the bottom are pretty solid. The nav and weapons panels are very unlikely to change between now and release.
I'd suggest if you want to get started early to plan the aesthetic design of the boxes, go for it. What we might do is an update soon where we state explicitly what's feature-locked and what isn't.