They're US style dates. I do like the idea of switching to the international date format, but I'm worried that might confuse people too.
Honestly, you can confuse people if you have more than one version, period. People can expect surprising things, and when they don’t find what they expect, they can get confused.
The thing about the ISO date format is that alphabetical sort ordering also sorts by the date. This means that as long as the earlier part of the filename is the same, the files will fall in a consistent order.
If someone will be confused with any choice you make, the best you can do is to have something that tries to help the user figure it out. The sort order will help both on Itch and on the local file system, plus a person doesn’t even need to know the difference between “it’s a version number” and “it’s a date” because the sort order is the same in either case.
The way to prevent confusion would probably be to go with an “Old Versions Archive.zip” of the old versions and to only have a single version of the PDF. I’ve seen some games go with that approach.