My number one criteria is "room to move". I wouldn't want to spec a bike that painted someone into a corner and gave no ability to go 5 to 10mm up/down with pads or shorter/longer with cockpit. If one bike has an athlete maxed out one way or the other then I want to look at the other size - if it works.
My number two criteria is handling. The "Front Center" on a bicycle is the distance from the BB (Bottom Bracket) to the front hub. With the way we ride a triathlon bike (lots of weight on the front wheel) - if the Front Center gets short then the bike can be a bit sensitive (read: twitchy). This is, of course, to scale - a tiny person has less weight on an appropriately small bike so it's not felt as much but if you're 6ft plus and can choose between two bikes then going with the larger one can have an advantage in handling.
Your Pad Y/X of 620/509, the Large bike with flat bar, short stem and pads all the way back on the stock mount yields a Pad X of 511 (with TSP you can go shorter). To get to your Pad Y of 620 (on the flat bar) you'll need three 5mm spacers and you're there. If you go with the drop bar you'll need a single 20mm spacer and a single 5mm spacer to get the pads to the same height.
I'm all about athletes mastering triathlon
Twitter - @TriCoachIan