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.
Having it as a benchmark is good, it encourages developers to aim to get good performance on a relatively underpowered device. I worry that an upgrade would muddy the waters... And drive games away from aiming for "verified" on the steam deck 1.
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.