IPhone – Does adjusting the volume in iTunes alter audio quality

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.

Start and stop times do sync, as well as volume adjustments.

EQ settings sync as well. However, they only work under the following conditions:

• You used a preset in iTunes (not custom EQ settings); and
• You have EQ disabled on the phone.

As backwards as that second one sounds, if you EQ enabled on the phone, it uses that EQ setting and overrides the per-song EQ settings. If you have EQ disabled on the phone, it uses the per-song EQ settings.