Neoprene roofing nails

I recently did a roofing inspection where the roofer had exposed roofing nails with neoprene washers in multiple locations. I’ve been trying to find out if this is an okay practice, or will the rubber seals around the nail heads likely fail due to temperature differences and be a potential spot for leaks in the future?

Additionally, there were asphalt shingles that were torn, some that were just not glued down, and the rubber boots on the vents had sealant around the top of the boot.

I know the torn asphalt shingles should be replaced and that the loose shingles are defects, but I’m not sure about the sealant around the top of the boot? Should I call this out, or is it acceptable practice? It appears to be a roofer that just didn’t take their time to do things the right way, but I’m just not sure. Any help/advise would greatly be appreciated! :D) Thank you in advance!