Okay, I asked the question and then immediately answered it myself. You can see in includes/fields/class-acf-field-taxonomy.php line 15 that the terms are saved to the post with a priority of 15. If you don’t specify the priority of your acf/save_post function, it defaults to 10, which will run before the terms save. The easy fix for me was the change my function priority to 20. Everything still works and now my terms are saving on new posts!
