I bought the Concours because of the physical size of the bike. Sure I could have put a taller seat and lower pegs on my Ninja 650R, but when I tried a pad on the seat the bike then felt different, like I was riding on top of the bike instead of on the bike. If folks would just buy a bike that fits them then there would be bikes for everyone out there. I laugh when I see a 6'3" guy on a Vstar 250 or even 650, and also laugh when I see a guy on an M109 that can barely hold it up.
Rriders with a few inches shorter leg lengths outside some magic design "norm" should not be artifically restricted to only toy bikes, small sport-only bikes, or cruisers. (It has nothing to do with standing height, it has to do with leg length only.) Just because a bike might fit leg length does not mean the customer is interested in that type of bike.
Lowering the top part of the seat-area-only part of the frame somewhat to accommodate the option for a lower seat would in no way make the body position any different for the rider than without such a change (with a seat height adjusted up accordingly). There is no necessity to change the tank height, the tree position, the peg positions, etc.
There are, of course, some very complex factors to consider in frame strength and positioning of other things to maintain the same rear tire clearance. But I bet it could be done. Even with such a change, it is certainly still not going to accommodate everyone, but expanding the possible market base is a good thing, as long as there are no significantly negative design consequences.