It never occurred to me before reading this comment that there actually is a use case for the execute permission. To me it was always just this annoying thing I have to do whenever I download an executable which I didn't have to do on Windows.
There's a bunch of zip implementations(Info-Zip, Gzip, 7-Zip, PKZip, Pigz, etc.), so perhaps an older version of one of the implementations didn't support preserving the Linux executable permission in the past.