Was New Roof Installed Correctly

Greetings! My family recently had a new corrugated steel roof put on our house. After the job was completed, I went up on the roof and found a small section of metal missing (in front of our chimney). While the area seems to have been well sealed with a rubber type material, it does not make sense to me that a area would be left like this on a new roof (without metal up to the chimney). Water was standing in the hole area, but so far there has not been any leaks. Given how much we spent on the roof/siding project, I just want to confirm if this is an acceptable practice? Much of the other work completed with the siding and window install was shotty, so I wanted to get some professinoal feedback on this? I asked the roofing contractor and they replied that the area was sealed correctly and intentionally allowed for heat to escape the roof. Please see the attached pic and please share your expertise? To me it seems that any material beyond the metal on the surface will undermine the integrity of the roof in the long run... Any and all help would be much appreciated. Not sure if or how I should approach the contractor... Thank You!

Who is the manufacturer of the panel? I would call them and ask for their chimney flashing instructions and present that to your contractor.

Eric, GREAT Idea... Already reached out to them....Thank you so much for this suggestion.