I was on the fringe of working with a fellow who was training for the NFL Combine (basically I put him in touch with people who could train him properly since that is far from my area of interest/expertise). I talked with one trainer about 40 times. This fellow had worked with many Olympic athletes.
He was pretty clear that 40 times serve as a way to set everyone to the same standard, sort of like the SAT/ACT. As a measure of what a person can do on the field, it is lacking. For one thing, how often does a person run a straight line, all out 40 in a game? Especially if that person is a lineman?
The vertical jump test is probably a far better indicator since it measures (to some degree) explosive power. A lineman for instance, may only need to run a few yards before he either initiates his block or gets to the tackle.
I think a 10 yard dash would be more appropriate. Organizations get stuck in the "we have always done it this way". Recently I changed a protocol in our lab situation to reflect what really happens in the sport. Of course there is no validation of the protocol yet (although we are getting there) which is problematic.
As for football v. track, I would say one could far more easily take a fast football player and train him to be a sprinter than a sprinter who never played football and teach him to play football. Being a receiver or RB in football is a lot harder than people think. You have to have football smarts. Not sure how smart one really needs to be to be a sprinter. This ignores the fact that you are going to get knocked on your ass on a regular basis by very large and generally feisty men.
Another factor that everyone is missing here is that even the smallest football player in the NFL is probably taller and weighs more than your typically high caliber sprinter.
For instance, Quentin Griffin is one of the smallest position players in the NFL (listed at 5"7' and 197 according to the Denver Bronco website--hell the Broncos KICKER is bigger!). Justin Gatlin is listed at USATF as 6"1' and 168 lbs). Gatlin is taller than most sprinters but the weight is in line with the quick survey of US sprinters.