Welcome to our forum.
NE Phil: The reason the drain is positioned 1/2" above the bottom of the footwell is because Marquis doesn't believe in putting plumbing underneath the footwell. From a design stand point it is a very bad idea because you would have the weight of the spa and all the water on top of plumbing. The small inconvenience of getting that last 1/2" out is well worth it compared to having a leak beneath the footwell that would be very difficult to fix.
To put a drain in the bottom of the tub it would probably raise the height 3 to 4 inches and then that does not mean the plumbing or the pumps would drain 100%.
Another thing to consider is you're never going to get all of the water out of a spa. With 500+ feet of plumbing, it is impossible to get it completely free of water, so why worry about the last 1/2" or so of water?
...because I can see it! I cannot see the water in the plumbing! - I already said it didn't make sense and, yes, I was being anal about it. Phil
If you have plumbing beneath the footwell and you have two spas side by side with the same exterior dimensions, the spa with no plumbing beneath the footwell is most likely going to have more interior depth.