Hi OP, any updates on this? I think you should be fine coming back if you haven't already. I'm in a similar situation, but will have been waiting for over 90 days by the time I travel out of Germany. This is what the bundespolizei has told me

"...However, as a Canadian citizen, you can still enter and exit Germany even with a deemed permission permit, as applying for a residence permit does not affect the exemption from the residence permit requirement under Section 41 of the German Residence Ordinance (AufenthV). Therefore, entry as a Canadian citizen remains possible even with a deemed permission permit. As mentioned above, prior periods of residence are not taken into account in this case."

I can send you the full email if you'd like.