I think the issue here is that
1) out of an abundance of caution, 7-zip warns if it sees a header that it must ignore because it doesn't know what it means, and
2) the game is compressed with a different program that adds a header that 7-zip doesn't know about.
The odds are that this is some completely unnecessary header containing information such as, "Compressed with version X of the Python ZIP module, using the following settings: ..." or "This archive was compressed on a Windows system". Probably a late addition to the ZIP standard not yet implemented by the version of 7-zip in question. Of course it could also be something completely absurd such as: "Does this really work? Can I really just add anything as a non-standard header? NOTE: Don't forget to remove this test code before shipping the final version of SuperZip2000!"
In other words, the warning is similar to when a hypothetical (we are not quite there yet) AI car mechanic robot asked to repair your car says:
"Before starting to service your car, there is a sticker on the bumper that I do not recognize. I cannot determine whether it contains information relevant to my work. By telling me to proceed you acknowledge that I am not to blame in the event of damage due to my ignorance of the meaning of the bumper sticker."
In the real world, everybody would laugh about this and nobody would obsess over it and try to remove the bumper sticker to get rid of the warning. Given the existence of malware I can understand why people who are not computer experts are more cautious in this case, but it's really pretty much the same thing. While the developer might want to consider looking for a tool that removes the extra header(s) without breaking the game for Linux users (as happens when you just unzip and rezip on Windows -- it loses the executable bits, which Windows doesn't know about), that would be the equivalent of a company removing all bumper stickers from its car because of the broken car mechanic bots.
The real solution is on the side of the players:
1) update 7-zip or use a different program for uncompressing (one that doesn't warn about unknown headers or at least knows all relatively standard ones), or
2) just ignore the silly warning.
It is extremely unlikely that the extra header has any information that is required for uncompressing the game correctly -- which is what this silly warning is for. Extra header warnings are not malware warnings, they just warn about potential compatibility issues. (The idea is: If you uncompress the game, ignoring the warning, and then it doesn't start, you can check if uncompressing with a different software helps. That's something you might not otherwise have tried, or not immediately.) It is possible that there is some malware in an extra header of a ZIP file, but given the frequency with which this happens and the fact that nobody seems to have any actual problem other than being scared by a warning, it's extremely unlikely.
