While the game plan may have been to run a certain set or type of plays, a good OC will amend the play calling to what the defense is giving you. If the run game is working, keep doing it even if that wasn't the original plan. The run game will always bleed the clock because they typically take longer from snap to whistle and the clock will only stop if the runner goes out of bounds. So what A-Rod said makes perfect sense. They must have planned to throw it more, but when the passing game wasn't consistent and the running game was working, they decided adapted the game plan accordingly.

I think your point about time management for play calling is also spot on. It seems like we take a LONG time to get plays into the huddle and then get to the line to snap the ball. That could be a symptom of poor game planning design (how A-Rod and staff have the plays laid out, like formats used to make it easy to find the right plays), poor planning pre-game to know what plays to have as your set game plan, your potential "Plan B", and then the rest. If he doesn't have that planned out he is essentially drawing plays from a hat until he finds the one he thinks will work, and that wastes time. This could be a reason why our substitutions are done so late in the process. There could be other reasons as well with regards to OC/QB communication and QB/huddle communication that need to be addressed.

It seems like they need to better organize the game plan, including Plan Bs so plays can be called quicker and quicken the communication loop. Also have defined options for audibles based on the situations. That could hamper play a little bit, but it seems like Jake may need that this year to help him execute, and as he continues to grow they can give him greater latitude. Kalani needs to have a deep dive into this process with A-Rod and the whole offensive staff and fix this. This is an Achilles heel for the offense that needs to be addressed. especially in the Red Zone.