Yes, exact same location, processor, amp, etc.
The difference in LF is significant. I always found the R11s to be a bit lacking, but the Reference 5s definitely made a tremendous difference. And yes, I also have 2 subwoofers but my main speakers still take care of 80Hz and above. The driver itself is a lot more transparent. It's hard to describe it, but the Reference really makes the music come alive, almost like it surrounds you or as if you're right in front of the performer. The Reference Uni-Q is fantastic. And then the build of the speaker: the R11 looks gorgeous, but the wood is very flimsy. If you compare these 2 speakers side-by-side you can easily see the difference in quality of the build.
Is it worth it? At MSRP I would say no (unless you can afford it). I ended up getting my Reference 5s used when the Metas were released and I got them for an absolute steal (say: a bit above retail of new R11s Meta). From that perspective it's an absolute fantastic speaker. But I won't be someone dropping 5 figures on speakers. However, the used market for Reference speakers is a fantastic and many bargains can be found.