In all of the other roof vents that I have seen, the entire width of the
bottom end of the vent flange is treated like a shingle, and is just left
exposed without any holes or exposed nails, which is why this configuration
is puzzling me.

Thanks for any help on this,

Jon

Here is an excellent video on how to install a vent on a roof. I
followed this when I had to put in a range hood vent.
http://www.youtube.com/watch?v=gee3itzjOG0