Unlikely unfortunately, they don't currently offer replacement motherboards at all.
When the ifixit repair parts initially leaked, they had a replacement motherboard available but priced at $350. Later when ifixit officially started ordering repair parts, the motherboard was no longer available.
My guess is that it wasn't worth selling the motherboard for $350 when a 64gb deck was only $400. I'd imagine the same issue would apply to an "upgrade" motherboard.
Why not? If you jump in now and get a deck you get better, more up to date hardware, as it should be. Also with a better chip its probably up to you if you want to use that to chase higher FPS and graphics or longer battery life.