That's exactly what I'm saying don't miss any! Pull or get the cut sheets for all the equipment that is going up there if you get the job.
Confirm with the GC and the HVAC that you understand X number of pentatrations will be done by you and ask when you can stub up your conduits or place a short run through the holes.
Some times the HVAC will cut and supply their own pitch pocket, but you said they are spec'd to you.
Roofers are like tile guys there here then gone... and they don't say good bye.