Having owned both and having put over 53,000 miles on my S1000RR, I can tell you that the 1229 has to be run in race mode to get all the power out of it. The S1000RR is the same in race and slick modes, it's just that in slick, the throttle response becomes a bit sharper, but the power is identical.
My S1000RR had a full Akrapovic race system, custom tune, BMC race filter and made 185 rwhp on crappy california gasoline and a very tired old engine, so they are VERY fast, but my 1299 is faster in every regard, other than maybe a standing 1/4 mile. I just did some roll-ons with a friend who weighs 10 lbs more than me on his 2015 S1000RR and he loses about three bike lengths to me and more; we shut it off at around 170, so we don;'t know if the S1000RR claws it back on the top end.
Either way, both bikes are stupid fast, but the 1299 in race mode comes on SO hard from about 5K rpm, that the BMW can't stay with it until it gets up to around 9,000 rpm; THEN it's neck and neck.
Cheers.