yes, that is probably ideal, but it is rarely done that way around here…
The glue strips under the shingle tabs usually dont seal all the way across though… There are usually small gaps between them, so that is probably where it gets through
Here is one from a couple days ago… This pic has both examples. But even the roof vent pictured is usually covered over.
That’s true i usually never see it either in Florida that’s why when i saw the video about at least leaving the front exposed to divert water i was like dang are all these roofing companies not doing it right? But you’re right i do see it a lot. My house, my moms, my grandma as well and this one. My grandpa is a handymen he told me it was under for cosmetic reasons and i didn’t know if that was true but when i looked it up it was true and but then that’s when i learned the front needed to be left exposed still always. That was like 2 months ago before i was licensed when I wasn’t sure but I’m leaning everyday
How much you charge ride alongs hahah
Good points. And since you see it often you would know if it is a regular problem. Oatey and other manufacturers demonstrate the bottom flange exposed. My thoughts water will enter high and disperse under the shingle…that is my theory 
I tired doing tons of reading on this, because i understand roof penetrations are the number one 1 a roof can leak
I also NEVER see step flashing here…
This isnt the best example, because its hard to see, but this was a brand new home:
I guess Florida is just backwards…
Apron flashing is always angle flashing in my area, too. And now, the IRC does not require step flashing either…angle flashing is acceptable on sloped sidewall. Crazy. That’s a clean install in your photos.
I telling you Florida is backawards cause I’m trying to make sure I’m doing right lol but sometimes i keep seeing the same issues. That’s why i always asked myself ok. The video I’m watching and article I’m reading. Does it relate to Florida? I know every state different and weather and all that. But i feel like Florida is so different lol
But Florida a great state for inspectors 
I’m like you to though. I don’t really care about what’s acceptable to much to memorize all the codes i look more for what’s the more practical and proper way something should function. I wont say it’s a defect, but i will say look this done, but it could have been done better because of this and this.
For now, focus on what does not perform as intended. Look for leaks, look for damage. And fill in your knowledge (careful of youtube and google) and learn who are industry leaders and lean on manufacturer installation instructions. (and experienced inspectors in your state!)
To @dhorton2 Daniel’s point about what is customary in your area and what is actually causing problems.
Here in GA, I see nails in the bottom half of boot vents all the time. Per the manufacturer, this is a no-no. However, I seldom (if ever) see them leak here. Therefore, I do not call this out. (I might if the sealant is old, cracking or failing). You are actively seeking ride along’s…Good!
Which is funny, because I had a city inspector ask me one time as I was coming down the ladder, if the flange was nailed or covered by shingles. He said when it is exposed, he will call it out if they are not nailed down.
(for wind uplift)
Lead pipe boots do not leak. Until, that is, the squirrels chew the top off… I see that almost every time a tree is next to the home. 
Yes sir understood
Why is their nails visible on the bottom of roof vents bad?
You think its cause Florida is a high storm state and they want the nails for stronger uplift?
It gets out, the “beauty strip” doesn’t seal the bottom edge.
Exactly right… 
Well…those of you in the field say it does not leak then I cannot argue the performance. But I would say manufacturer guidelines and common sense would argue if this flange is under the shingle then you have not really flashed the protrusion. Lapping of shingles and flashing is kinda 101.
If this flange is under the shingle then you have not lapped anything. You have just added metal underlayment. Maybe that is why there is so much sealant around them.
