1. Gitlab is able to migrate up to a new version, so is there anything preventing it from getting up to a certain (older) version before running the last few migrations after restore?

If I set up a new instance it’s generally one or two minor versions higher than the old instance.

2. I swear I restored from my omnibus installation to Helm based gitlab and lose all my uploads and registry images. Cannot see from the docs why that would happen any more though.

Maybe it was the opposite, with me restoring the backup to the same block storage devices, and gitlab hiccuping on the fact that all the files it wanted to restore were already there.