Make iTunes song options stick on other devices?
While I'm not sure why the options aren't being kept between your device, there is no way to make iTunes edit the file itself. Nearly everything Apple makes revolves around the idea of revisions. iTunes, while not using revisions, only edits it's database to mark the in and out points of tracks.

To correct syncing, I can only suggest removing the song from iOS and adding it back (it doesn't rewrite data for tracks already on the device).

The get around this, you can always edit the file yourself in something like Audacity, if you wanted to go the permanent route.