Apple is reportedly not accepting apps submitted using beta OS X, Xcode or SDK versions. Not sure how they check.
So if you want to submit an app or update in the near future, wait until after the GM releases, and Apple's "GM is OK for submission" email.
Or maybe set-up a dual boot system, VM or 2nd Mac for all the beta's, and use source control to keep the beta from potentially messing up your code and build files.