What is the technical explanation for why Archive Utility can break certain apps, while other unarchivers won't?

I just experienced this issue described in this answer . I had downloaded a zip file containing a macOS app , and first unzipped it with Archive Utility, when trying to open the app, I got the error that it "could not be opened" (with no further clarification) just like in the Q&A linked to above. However, when I used Keka (third party archive software) to unzip, the app worked just fine. What is the technical explanation for this? Aren't zips and other archives supposed to come out literally the same, byte for byte? How can one unarchiver break the app, but not the other? I use Catalina on an Intel Mac.