[Deerfly]

Workmanship looks pretty poor, they knew the TPO went on the top of the structure, but that seems to be about it.
Lots of wrinkles/ fishmouths in the seems, addressed incorrectly with the caulk as well. The seems all look to be handwelded. Looking at the way most of the details were completed I'd expect them to be half assed as well.
I'm guessing your not getting any sort of manufacturer warranty with the system.
What type of substrate is under the membrane?

 

[Deerfly]

I would, I am not 100% certain how GAF inspects their roof systems for warranty. When I installed Firestone Roof systems, every roof was inspected. We installed 1000's of squares a year.
Most times the inspections went well, minor infractions would be addressed at the time of inspection if their was any, and a company employee with on the inspections would make repair/changes on the spot.
If the inspection was done without an employee present or the punchlist of repairs was to time consuming to repair during the time of inspection, we would go back at a later time to complete needed repairs to comply with the specs/details required for warranty.
Pictures and detailed notes were logged on a laptop/tablet for repairs required. Until repairs were completed, warranty were not issued.