I also engine brake when slowing and haven't noticed any issues. That said, I had already done the switch on my race bike and had a good bit of practice doing 'downshifts fired in anger' at speed before switching the street bike. But with the Concours, there is a good amount of engine braking so a couple of quick clicks up on the shifter do pretty well to haul her down from speed. The more pertinent advantage though is pretty much never missing an upshift since you're pressing down with your foot vice pulling up with your toes.
The old Nortons (while the shifter was on the right instead of left...) had a 1 up, 3 down pattern as stock. It just makes more sense to me to use the more 'positive' shift (i.e. press down) for the act of changing up to the next ratio, as this action is where the transmission is more likely to be under load conditions. It's one of those things that once I did it, I thought "Why don't they do this stock? It just feels easier..."
As a corollary, have you ever ridden a cruiser with a heel-toe setup? Even when I can operate the front part of the lever like a 'normal' shifter, I tend to find myself stomping down on either side both for upshifts and downshifts; pressing down is a more 'positive' action.