It does, Rockstar optimized their game to fetch data from both the hard drive (the mandatory installation) and different data from the optical drive at the same time (2 different buses), thus producing the best result. If you install both the discs on the hard drive, it becomes sort of a bottleneck and it isn't able to fetch the data efficiently and fast enough, causing pop-in. If you install the play disc to the USB flash drive that problem is solved as it will still fetch data from 2 different sources.
This has been the case with a few games in the past too, Halo 4 had this, but much less noticeable if I'm looking at Digital Foundry's videos.
Very interesting, Thanks for clearing that up