I think Itch's default file count cap (1000) should be raised a little bit, because currently it's too small for a stock RPG Maker project. Make it 1500 or 2000. The total file size cap is fine - it's just the number of little files that's a problem.
A blank project in RPG Maker MZ starts off with over 1300 files due to the built-in database. In terms of disc space, this sort of empty project is fairly small (98 MB), it just has tons and tons of little files. RPG Maker has an export-to-web option, but an out-of-the-box project cannot be put up on Itch due to the file count limit.
RPG Maker doesn't do a lot of asset sheet consolidation (the editor doesn't support it for anything but a few fixed-size character spritesheets). This means (for instance) that the 'pictures' folder is 120 individual character pngs, there are 210 files with stock enemy pngs, 175 files of attack animations, et cetera.
If Itch servers have deduplication set up, the RPG Maker stock assets should add virtually no additional overhead anyway, since a deduplicated image takes up the same space on disc regardless if 10 projects or 10,000 projects are hosted.