What you experienced was a difference in rider not bike.
Thanks... Seriously though, I had the opportunity to ride the same track, with roughly the same cast of characters on my 1199 base model. It was fast, but not overtly dominant. The R, with full pipes, does spin up with a more impressive degree of fury that seems to be able to dispach anything else out there, including the 1199S's, with ease. There were several S1000RR's and a couple HP4's out there. I have no formal roadrace experience, and I'm turning consistent 1:15's with a best of 1:15.1 at PIR on the thing without scaring myself, and still improving rapidly. I put it on Dunlop slicks, but I have left the suspension settings alone so far, because I don't know how to make it better. I think that says a lot about the bike and factory setup. I have totally worked over the base model bike, including ride height, to try and get it to handle half as good as the R.
P.S. I know everybody has their own opinion on tires, but I believe the bike handles way better on the Dunlops. There is no sensation of transition into turns like on the Pirellis. It's like the geometry stays the same now, regardless of lean angle. It does take a tad bit more effort to muscle it down, but its way more stable and confidence inspiring, like I go 10-15 mph faster in the sweeper.
To me, the HP4 looks like such a monstrosity compared to the 1199.