One might argue that ownership made it an issue with him in the first place, and that subconsciously, Flores partly took it out on the 2020 1st round pick "they chose" and made his life a difficult, agonizing, painful hell as a way of getting back. Vindictiveness can be such a cruel, mean-spirited, and petty set of emotions mostly.
I'm not saying or arguing that if actually true, Flores approach here is in any way rational or logical, it isn't. But NFL HC's are and can be very quirky, peculiar types who want to win "their way but with ALL their guys" and since Tua wasnt one of Flores "players", and was forced upon him by the organization, his ego and pride influenced him to treat him like burnt crap on occasion.