Installing new DWV system, finally ready to cut the stack through the roof. The flashing/boot that I bought says "do not caulk". I assume that means don't use caulk around the neoprene gasket that seals around the stack pipe, makes sense to me.
But what about the flat underside of the aluminum flashing itself? I would think that a bead of sealant around the perimeter would make sense, so no rain rolls under it and into the hole in the roof. Any thoughts?

If the shingles are properly nailed down over the top of the boot, you shouldn't need caulk or sealant. Of course, it often seems they do leak. Adding the boot to an existing roof makes leaks even more likely. I would seal the upper side to the roof. A friend has me trying a elastomeric sealant. Don't know if it will last better than the old roofing cement. It is easier to clean up after using.

Don't seal around the neoprene. Do seal under the exposed bottom edge of the flashing. This will help with any wind blown rain.
The bottom of the flashing should be exposed so no water/snow gets trapped and backs up under the shingles surrounding the flashing.

I have to replace 2 vent flashing boots on a customers house this week. The neoprene split and rotted away and water is following the pipe into the house. Only good thing is where it leaks through the ceiling it drips right into a bath sink.
Of course I can't do it today... its raining.

Thanks. I was able to get the top tucked under the shingles above it, I used roof sealant under the flashing all around. After I was finished, thought crossed my mind that I shouldn't have run the bead of sealant all around the flashing, rather leave the bottom open so any water that penetrates the sides can continue to run down. Should I remove and re-do it?

Also, I've seen houses that have the shingles covering the sides as well as the top of the flashing pan. I assume those boots were put on before the shingles, whereas my roof was on first. It rained all day here yesterday and not a drop came in, so I guess I'm OK now.

The flashing should be covered by shingles on top and the sides with the bottom exposed. Your right as far as those you saw more than likely where installed prior to the shingles or they were replaced by removing the roof shingles around the vent and then replaced.
When I replace the flashings I also remove the shingles around the vent so it can be flashed the proper way.

BUT... if its not leaking and you sealed it up well I don't see a need to re-do it. Just check it in a couple months so everything looks good.