Apple waves fees for non-profits (both developer annual fee and core technology fee), so at least qualifying free software organizations don't have to pay anything for either the app store or alt stores.
Free software organizations don't package software. The people developing iOS ports of FOSS applications are not going to register as a nonprofit to play Apple's silly game. It's an insult of a fig-leaf to the industry at-large.
Plenty of free software organizations package software. Heck Mozilla, Signal, VideoLAN, Mastodon, Wikimedia and Tor even package iOS software.
And frankly, most of the iOS ports of FOSS aren't themselves are closed source, so they don't really count as FOSS, but if the people who, say, ported OpenOffice to iPhone gave it to the Apache foundation? I can't see why they wouldn't release it.
https://developer.apple.com/support/fee-waiver/