Interesting approach. This surely would avoid the challenge of having to 3Dify a 2D organism. A downside to this however would be that in every playthrough at some point all multicellular organism would be one cell thin pancakes, films if you will. This isn‘t quiet how it was on earth and it would be strange if it played out like this on every single planet.
Additionally, as you already said, many body plans that worked in 2D would be thoroughly messed up by this. Imagine you gave your organism some sort of mouth indentation at the front so it could accumulate food inside. This would be rendered useless when entering 3D space in the way you proposed.
Oh, in this case I missunderstood you earlier on. I thought you agreed that specialisation should occur only after the dimensional transition. Do you think the benefits of early cell specialisation outweigh the additional challenges we will face when working on the dimensional transition?
Or do you disagree with my premise? Do you think the dimensional transition won‘t be any more difficult than it already is by having specialisation occur before the transition?