As an update, my partner got in touch with the person we've been working with in our MP's office. She didn't seem overly concerned and said that when end of the standard processing time draws near, the email is auto-generated. I haven't heard this before, but that's what she said.
She seemed to think things would still be processed in a relatively timely fashion, not too far out from our current processing times. Given that on Thursday (which was 11 weeks in) she was told by the Home Office that we had no flags, and then on Monday, 2 business days later, we were suddenly too complicated to process on time, I'm hoping that's the case.
Anyway, she did say she'd call again to find out more. Still, it took 2 weeks for her to get a hold of anyone last time, so maybe I'd get a decision before then. I can only hope....