Overall however this seems to show a shortcoming of the legal framework around this stuff; it wouldn't be unreasonable for it to be possible for the author of some program to accept responsibility for copies made by Apple.
A separate problem seems to be the issue of restriction. This is a little thornier. I wonder would it be enough for the program, when downloaded (direct from the publisher's servers, using the App Store as nothing but a directory), for the program to show a notice saying "this is free software; source code is at X along with instructions for running it on this and other platforms"? Figuratively this would leave the user empowered to do anything they could with ordinary free software; the fact that the presently running copy can't be modified in situ ceases to restrict their actions in any meaningful way.
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