I think it's okay. They are different namespaces and people should fix their bugs. It would be like skipping the street number "911 Foo St." because "911" is the emergency phone number and 911 Foo St. is just a regular house. I'm sorry if someone is confused but they shouldn't be confused. They're totally different things.

The biggest mistake we made with DNS was the "shortcut" of implicitly adding the root domain to random strings treated as domain names (turning "example.com." into "example.com"). The file "foo.zip" and the website "foo.zip" wouldn't even be ambiguous if we called the website "foo.zip.". "ndots" also causes operators of DNS servers a lot of pain -- some malfunctioning program tries to resolve "example.invalid" in a tight loop and it balloons to asking for "example.invalid.", "example.invalid.local.", "example.invalid.cluster.local.", "example.invalid.svc.cluster.local.", and then DNS blows up, breaking everything.