People seem a bit confused. There are a few separate legal questions here:
1. Whether Congress can ban noncompetes nationwide through its ability to regulate interstate commerce.
2. Whether Congress can say "so-and-so can make any laws he wants about x".
3. Whether this is in scope of the FTC's mission of preventing unfair trade practices.
To me, #1 is a clear no for intrastate agreements, but under Wickard it is constitutional.
#2 is yes under Chevron.
#3 seems an obvious yes.
The only question would be if SCOTUS decides now is the time to correct what it sees as prior incorrect decisions.