I bought one of these Ultimate Pipe Flashings vent boot flashing units which come with these nail slots to secure the unit. Part of their instructions is to only fasten with nails within the slots designed into the unit.
What I'm curious about is whether or not its a bad idea to nail a vent flashing in areas that are exposed, ie not covered by shingles, even if you caulk the nails.
Nailed Flashing Examples
Here's some examples where I'm seeing them installed with exposed nails.
I would think even with caulking its a bad idea simply with expansion and contraction of the materials at different rates which should wiggle out the nails as I see in my family's roof if you look at the warped and wavy flashings in this image. (I believe all the flashing is original to the roof, so some 40+ years old). I also noticed with the examples that the nails eventually rust and would consequently shrink and allow water to seep as they lose their bite onto the sheathing.