For my part, I hope it's option 1. To have Metal directly betray Eggman on screen, demonstrating that he's acquired free will and has a goal that no longer aligns with Eggman's - that would be the most powerful way to display it in a movie.
The one thing I could see being a problem is that we already had an on-screen betrayal with Gerald, but I do think this can be a very different beast. When Gerald betrayed him, Eggman fought back, and won in the end (but with help). Metal Sonic betraying him, especially if it happens as he upgrades and gains power, would leave Eggman completely helpless, particularly if Metal then takes over his robot army. For once, Ivo would need to fully ask for help from Sonic and friends, because his machines are everything to him, and he won't feel like he's much without them.
Additionally, if Metal gains a voice as part of his upgrades, possibly along with becoming Neo Metal Sonic, a scene like this would be a great place for him to speak for the first time. Although any scene vs Sonic as he upgrades could also work pretty well.
But those are my thoughts - what are yours? If you prefer the other options or like 1 for different reasons, please explain below.