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And does it function like Windows 7zip, as in it can ignore repeated files after one prompted.
unzip -o
See https://linux.die.net/man/1/unzip
Edit: Kinda sorta looks like PCManFM-Qt auto-skips when configured to use Engrampa. (In fact it doesn't appear possible to make it ask - you can either auto-skip or auto-overwrite. I guess if you need "ask" you could configure the file manager to use a different archiver.) I mainly use the terminal so I might not be the best tester.
Afterthought: I somehow got the impression that the OP specifically needed auto-skip. I should have asked for clarification. If auto-over-write is OK, my initial impression is that some of the other archivers have a persistent setting for that. But I didn't test it.
https://i.imgur.com/RhMBKw9.png
it is totally not an issue with "linux file system" lol, or linux itself.
Linux is just a kernel, and file system in wide sense a combination of layout of data on a storage media, and a driver (or a kernel module) that reads and writes data from that media, and apart from doing that, it leaves all decision making to file management programs and user's input.