Bash 3.2 is distributed under GPL Version 2. Bash 4 is under GPL version 3. (I'll let others discuss the differences and how they might interact with the App Store.)
That doesn't make any sense, App Store has no relation to what Apple distributes as part of macOS.
Apple takes issue with patents-related wording in GPL3 and doesn't want to be subject to GPL3 (while they're OK with GPL2). Hence not distributing GPL3-licensed software.
[0] https://www.quora.com/What-is-the-reason-for-some-of-the-Lin...