The issue is the tool can't magically know whether, for example, a 64x64 PNG file is a 2x resolution image that should be resized to 32x32, or an image that's intended to be 64x64 at 1x resolution and is just really big. Of course, during actual import of a Lemmini set that's another matter, but when importing from lone PNG files there's no way for it to know, and there should probably be some way that the user can tell it.
I can add options that would help with this (and will look into what might work well), but can't make the tool magically know everything.