The issue is the coolant trapped in the core when the thermo closes. The trapped coolant gets close to the ambient temp.. Rain (the mass of cool water getting into the radiator is the same as riding it in extremely cold ambient temps.. If you search, you will find that the temp swing you are talking about has been discussed several times when the temps are really low. My 03 only has 6 bars so the temp gage does not show fluctuations, gen 2's have 8 but still do not show the swings that ARE happening inside (each bar [6 8 or] reprsents too large a change) however, my friends 02 Concourse has an analog gage that starts to dip in a very regular patterns (45 to 60 seconds) whenever the temp is under 40 and it gets really crazy under 20. It all has to do with the coolant that gets trapped in the core. I have considered drilling a small hole in the thermo to allow coolant to continue flow even when it was closed. Unfortunately this would result in the engine not comeing up to temp at all during extereme conditions.
My 03 dropped to only 1 bar, going down the Shasta grade, in the rain, once, it also stays at 3 bars when the ambient temp is anywhere from 95 to 115. (I havn't ridden in anything above 115)
Since this has been brought up so many times I predict that Yamaha will change the display in the next 4 years or less to the fluctuations are not visible to the rider.