I think the only way to answer your question would be to weigh the whole packer after trimming it, but before smoking. Then get your calculator out. Let me try some algebra here, might make me dizzy.
Whole Packer @$2.69/lb
PACKER = FLAT.
$2.69x = $4.99y.
x = 1.85y
So to break even you would need a trimmed, presmoked whole packer to weigh 1.85 times more than the flat that is trimmed by the supermarket.
Now here's the test. Let's say you buy a whole packer that weighs 15lbs in the bag ($40.35). You then trim away what fat you would prior to smoking and weigh it. Then you need to separate the flat from this same brisket and weigh it by itself. If the whole packer trimmed is not at least 1.85 times heavier than the flat portion you took off, (of course this is assumin your flat cutting is equal to what the butcher at the supermarket would do) then you paid too much.
I think I got that right, my head hurts. However, intuitively, I would say that the whole packer is a better value, you get more meat because of the point, I imagine a meat market has to grind that meat up or throw it away after separating a flat. So in that individual flat you are paying for prep/cut work as well as discarded meat that you don't get to eat or make delicious burnt ends from. And you get to control the amount of fat that covers your flat portion, as opposed to the butcher determining that for you.