There might be an appearance difference between some model years, but there's no fitment difference on the rear caliper on any FJR. They are completely interchangeable.
Personally, I think any differences (the drawings show the bleed screw in a different place) are supplier differences. Comparing the current fiche on Yamaha's site, the drawing is identical for 2003 and 2012. The part numbers for a complete caliper assembly are different, but the pistone, seals, and even the bleed screw have the same part number.
It is strange though.
