I've now looked at a few more and guess that they never run with the 64x64 resolution internally or they forgot to round off the positions. It is possible that with certain engines it becomes more and more difficult to set the games to such a resolution or to handle exceptions (e.g. font rendering).
Viewing post in webplayers don't render correct
A lot of people have the same issue with native versions, and the solutions for things like Unity are rather convoluted. So I think even if they get it working naively, they just assume the web export matches even though it may not. There's a bunch of web games that run through Unity player and others that get it right though, and some where sometimes it's right and sometimes it's wrong. So could be a lot of things.