Darrsi, no and yes respectively, one of the first things I did when I went back to the 600 was to search for a replacement rear caliper. It's also the sensitivity of these calipers that is important; I always felt like the standard rear setup had wooden brake pads & I could not sense when it was about to lock up. And that was despite still-moving pistons. The 43mm piston rear calipers are surprisingly easy to control.For the cost of new replacement Yamaha seals you can have an alternative caliper, so for me it was mandatory not optional. And if you don't observe a very strict cleaning regime a couple of times per year, the original caliper seizes up.... whereas I can be a lot lazier & overhaul mine every 18 months or so
Darrsi,As the complaints about standard rear calipers are rife (and have been for the six years I have frequented this site) I would infer that your enthusiastic cleaning efforts place you in the minority I suspect that most people aren't as keen as you to tackle their rear calipers quite so often, with predictable results.
On the pistons yes, on the back of the pads I thought you could use either? Slapped a load of copper grease on the back of ChristoT's pads and it stopped the annoying squeak he had - though he was a bit generous with his application of it :P