Gareth,
Your Pad Y of 596 and Pad X of 490 could work on all three sizes but we have to pass on the size Large because that Pad Y is the absolute lowest the bike will go (drop base bar, zero spacers) and you mentioned that you’d like the ability to perhaps go lower in the future.
Here’s the details for the Medium: Flat bar, short stem, a single 20mm spacer + a single 5mm spacer under the aerobars - and, the pads back all the way on the stock mounts (if for any reason you had to reduce your cockpit in the future you could employ the TSP). The result is a Pad Y of 595 (just 1mm off your number) and a Pad X of 489 (again, 1mm off).
The Small would look like this: Flat bar, short stem, two 20mm spacers + two 5mm spacers under the aerobars - and, the pads forward all the way. The result is Pad Y 595 (1mm off) and Pad X of 493 (3mm off).
You should do the Medium. I have two issues with the Small under you: 1) 50mm of aerobar pedestal creates a bigger gap between your arm pad level and your pursuit bar level - it’s just a ways to go to get to the brakes. You could do a Small with the rise base bar and only need 30mm of pedestal but I believe the bike comes with the flat bar so you’d have to purchase the rise bar to make the change. 2) I don’t know the Front Center measurement of the two bikes. The geometry chart online doesn’t list that element, but with some presumption and some basic subtraction I’m pretty sure the Front Center on the Medium is ~30mm longer and this would likely mean that you’ll enjoy the stable feeling of the Medium over the Small.
Ian