What really would not be fair is if games that break the rules would be officially ranked higher than those that follow the rules.
I don’t know, I feel like if the judges/community ranked the games that highly, that should take precedent over a wall of text that doesn’t have thoughts or feelings. If the community really only cares about games that follow the rules perfectly, then that would be reflected in the rankings and it wouldn’t be a concern anyway.
I don’t see how these disqualifications are anything but disrespectful to people who worked hard on their games and demoralizing when they don’t even get to see their contributions alongside their peers, even if they are at the bottom of the list. Waiting until the end of the voting period seems especially cruel, because they were able to see those ratings come in. Maybe you should comment on their entry on day 1 and at least give a heads up that the numbers won’t matter.
It’s also worth pointing out that there’s no messaging on the jam page about the potential for disqualifications, so for a lot of folks it seems totally unexpected and confusing, especially when there’s no direct reasoning delivered on a case-by-case basis. Posting a blanket statement on the Discord isn’t enough - it can’t be expected that everyone has joined (or even if they have, that they’re actively reading it). If someone’s work is being taken off the list, the least you could do is speak to them directly about why you feel it’s necessary.
I know I personally joined simply because I like dungeon crawlers and thought it would be fun to make one. If my contribution isn’t valued, then maybe you’d be better off making future jams unlisted and advertising exclusively to your Discord community. Or changing the name of the jam to something that feels more exclusive and exacting, so other folks don’t similarly read “Dungeon Crawler Jam” and find themselves shocked when their interpretation of the genre doesn’t meet expectations.