Hi Alexey, Paulov,
Thanks for your comments. This post is from last year, so possibly current Photoscan versions are faster doing the processing. We eventually split everything up in 3 chunks, the largest one with about 4000 photos. I didn't quite remember the processing time, but it was multiple days, mainly due to estimating scene structure. Our PC was a core i7-2600, so not that much slower than your model unless this step also relies on GPU.
After that project, we didn't process any data set close to this size. On typical datasets of 500-1000 photos the geometry reconstruction takes most of the time.