This entire situation is part of why I think you try to limit how much you put on the shoulder of the QB in the first place, and I've been saying this for a couple years now, how much freedom the QB has to make the play call.
I get it, you need to be able to audible, you need to be able to run the RPO, and these things give some leave way to the QB. But you also need guardrails. One is that the play caller (which should be the OC) needs to be able to assert himself well enough that the play calling reflects what he wants, for instance more balance in the offense, less QB runs, etc...
The other is you just can't put too much on your QBs shoulders anyway, especially if they are a dual threat QB. This is easy to understand when you think of it in terms of sheer math. If I have a QB trying to read the defense and make an audible if needs be, then decide how to run the RPO out of that, if he's pro style, he's just basically choosing run/pass and all his choices are based on that.
If he's dual threat though, he's now reading the defense, making adjustments, doing all these things with a third variable, run/pass/QB run. It makes it much more complicated. From binary to ternary. That's over 50% more information to process.
If you take a QB and ask him to account for nearly 70% of the offense, basically winning the game is on his shoulders, then you let him have information overload, trying to process way more information than a pro style QB, you're putting way too much strain on them. The OC and the run game both need to do a better job of taking some of that burden away.