That can happen regardless of which storefront you use to buy a free app. It's more of a developer-specific nitpick than a chronic problem with FOSS and freeware.

If you're happy to sponsor the app's development, then owning the App Store version should make you feel proud. The developer is still able to make a living thanks to you, and they're offering extended support if you're unwilling to use a fork of the free version. A good example of this is Dwarf Fortress, which I have bought on Steam 3 times now so that I could gift it to two of my friends. God willing, nothing will prevent me from buying a 4th and 5th copy when Christmas rolls around.