I don't upload it as a ZIP. itch.io does that on its end as I use Gradle to upload the folders of the loose files.
I have to upload multiple files together, i.e., for stuff like the SFX sources as a clearly-labeled file due to creative commons attribution license or else I cannot use many SFX I have, the changelog (a lot of websites scrape uploads without linking to the changelog), and the flowchart.