But on the empeg and in Jemplode, they would go back to alphabetical. Jemplode doesn't seem to care about the filenames, it cares about the song name in the id3 tag.

Hang on. I think you're confusing alphabetical screen order with playback position order. The empeg screen will list things alphabetically. The Emplode/Jemplode screens will list things in the order of whichever column you've clicked on. The important thing is what order they play back in, and that's controlled by the position column, which is controlled by the file name on playlist import like you say it doesn't do.

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