The difference is the output format. I created SingleFile before Chrome supported MHTML files. At that time, to save web pages in a single file, the only technical solution in Chrome was to implement something like SingleFile. The advantage of HTML is that this format is much more durable though.
Yes, there is .mhtml but it execution plainly sucks because it didn't exactly saves everything. It would attempts to save but it won't be valiant at it, it is like using mhtml without "force (-f) argument".