Considering Gibson was the one thrown out there against UVA and to start against FSU I think it's safe to say the second theory doesn't hold. Sims wasn't benched because they thought the back up was better, and if they thought that was true about Pyron just Because of a performance against one of the worst P5 teams in the country then I don't really know what to say.
But to me, the appearance of this doesn't look good for the coaching staff. Sims wanted to go back in against UVA and wasn't allowed. He was told he couldn't for health reasons. He then sits the rest of the game against UVA (Where Gibson does nothing, we lose, and don't see Pyron at all), FSU, VT, Miami until the fourth quarter when Pyron gets hurt. To me, that seems like the coaching staff was going to have Pyron play all the way against Miami and likely UNC, and then Sims would be healthy enough to start right in time for Pyron to redshirt and Sims to take the beating against UGA, both on the field and from the fans.