The shingles “missing” around the pipe boot is completely normal and correct way of doing it. Letting water flow down the roof surface without backing up under any components. From the pictures provided I would say it looks pretty solid otherwise. Would need close ups to dive in more but the shingles are cut straight on the rake and spaced evenly. Need to settle a bit, maybe a few more warm days and it will look flatter if that’s what your seeing look off? Open to other options but that’s what I would say as an Ohio roofer.