I can confirm that by disabling turbo you're given far more thermal headroom for the GPU by about 10-15 degrees celsius. Considering the GPU and CPU share the same heatsink and are spaced less than two inches apart, it only makes sense that the temperature of the CPU influences GPU temperature (pretty heavily).
I've noticed that games like Just Cause 2, Bioshock (yes it's an older game), GTAIV, Crysis, SCII, ArmaII, are all pretty heavily CPU-bound games, and as such, you'll see drops in fps when you lower your multiplier in Throttlestop. However, even if left at stock values for the sake of a higher fps, the CPU's temp will rise to around 88-89C while gaming, which would raise the temp of the GPU to above the 74C mark and subsequently cause GPU throttling-related stutter. When you lock the multiplier to say, oh idk 23-25x, these same games raise the CPU temperature to only about 77-80C, again allowing for more GPU thermal headroom.
I think this throttling issue stems largely from the fact that the CPU and GPU have different Tjunctions, and likewise rise in temperature up to the Tjunction relative to the load. So if the CPU is loaded up with Crysis, it's going to start hitting the 90C mark and heating up the GPU. I've read through anecdotal evidence that the Tjunction for the 650m is much lower than the CPU, with some forum posters @ guru3d suggesting to keep Kepler cards under 80C.