I'm not a roofer, but I'd have the vents installed the correct way. Even if it was sealed well the whole setup looks sloppy and prone to leaks. Show the boss or forman of the roofing company the pictures of the work you dont like and see if they'll fix it. If not you could look up your local laws, the roofer may have to make this right. If they do then document the work and make sure it's good. Either way I'd fix it, you don't fuck with your roof.
Sewer Vent Through Middle of Standing Seam ( sh.itjust.works )
Recently had a new standing seam metal roof installed. Roofers could talk the talk but I was not impressed with the quality of work overall....