If you check the deleted scenes for TND, you'll find there wasn't any extra plot development that was taken out due to pacing reasons, just dumb jokes which were better out of the film. And TND was longer than QOS.
Not every scene cut from TND was included on the DVD. The Stamper pain/pleasure stuff was definitely filmed (note how the edit avoids shots that go too close on his differently-coloured eyes).
I've got the TND final shooting script and it's got no reference whatsoever to Stamper's predicament. It definitely was in the script at some earlier point but how do you know it was actually filmed?
The eye stuff's a give-away, just because if his back-story was gone, so would be the make-up effect. (Ooh, my grammar kinda went wonky there!) But also, a few years ago I worked in around Pinewood/Shepperton and had a couple of drinks/chats/lunches with a few current or former crew members and department heads. One guy still had, at that time, the 'gold' that was built for the theft from the Chinese - sat in his storage! They'd had it made, and then it was cut.
I don't doubt the likelihood of some (or even most) of the scenes were dropped during shooting. The script was in ridiculous flux, after all, so they may have done one or two pieces and then packed it in. (I never asked about heavy specifics for fear of seeming to fannish.)
Not sure when the final script is dated, but presumably if truly final, it's close to the end of shooting?
(I've kinda wandered us from the 'QoS runtime' point, haven't I!)

