The PCIII was replaced by the PCV in 2009. That's why you don't see anything for the PCIII past 2008. AFAIK, the wiring connections on the bike are the same for all 2006+, so the PCII will work fine with 2009+. DynoJet just wanted to simplify their support obligations by limiting the PCIII to 2008 and earlier, and not testing their new PCV with any older bikes at the time that they introduced it. The PCV for 2009+ FJRs will also work as far back as 2006 on the FJR.
But that's just physical/electrical compatibility...
The stock fuel map for open loop mode may have changed a bit over the years, so it's possible that the PCIII map for your 2007 would not be ideal for a 2012. The way you could work around this is to download a PCV map for a 2012 from DynoJet and put it on your PCIII. This will most likely be a manual process: open the 2012 map in the PCV software, copy/paste map into a spreadsheet, delete any extra throttle columns in the map (PCV maps may have more throttle positions than PCIII maps), then copy/paste from the spreadsheet into the PCIII software.
Of course, you may ride your new 2012 and decide you don't even need the PCIII.
In 2008, the throttle cam on the throttle body was reshaped to give the same effect as adding the G2 throttle tamer to a 2007. There are also reported improvements to the fuel injection system for smoother part-throttle response. Note that this is most likely changes to how/when the bike transitions between closed loop and open loop mode, not necessarily that the stock open loop map has been changed. When using the PCIII/PCV as instructed, you completely remove closed loop mode by disconnecting the O2 sensor. Because of this, it is quite possible that a PCIII map for a 2007 FJR is just fine for a 2012 FJR (but compare the maps from DynoJet to be sure).