I will say this. My doc university's ETD dept is, how you say, le dumb? So, it was told to me that before I got too far along in the process to understand both how my committee wanted things formatted and how the ETD dept wanted things formatted. They are not professional writers, and they are not necessarily right. But they likely have a workshop and/or a manual. And honestly, even after you defend, you still will have to get your **** through them. I had stupid holdups both at the masters level and the phd level with this crap.
ETD does not care about APA style. And they do not use their brains. And they will be offended that you attempt to use your brain. Just do their format. Best case scenario is that you can explain to your committee that you are writing in a certain format for ETD at some point and they'll get on board with that.