MS already allows you to unlock the ability to run custom code on their hardware for a ~$20 fee. Sony doesn't seem to do this yet, but on the other hand, they did eventually get the disk drive version of the PS5 to not sell at a loss.

So, I don't think it'd affect them too much. Alternative stores would mainly just end up being convenient for small indies and homebrew developers, neither of which would've been able to afford the fees to get onto the official stores anyway.