These are pics from my Father’s roof. He had an addition built several years ago and had the entire roof replaced as part of the work. Is there any situation where the flashing is correct on the skylight “bubble” and the vent? The last picture is from the same roof, but over the original part of the home. I checked the attic where the vent exits, but there was no visible water damage. I couldn’t check the skylight in the attic due to the multiple roof planes.
Yes the flashing is incorrect. the flashing should be exposed at the bottom. The one vent seal looks good but has caulking at the bottom, which leads me to believe that it has leaked at some time. Here is a correct example.
It’s possible that the lower flange of the flashing overlaps the shingle in the second course down, but doubtful that you couldn’t see some evidence of that (like bulging or interference with bonding) by looking closely.
If it is installed that way, it’s a good installation because the nails through the flashing are protected, at least to some degree.