Okay, have run through this a couple of times now - first things first, I'm running the PS3 and the Sony BDP-S550 into my Onkyo 905 amp and this then feeds into my 42" HD Ready Panasonic TV. Both Blu-Rays are running at 1080p, leaving the TV to downscale to its native resolution of 1024x768 (I prefer this setup after trying out native 720p feed from Blu-Rays a while back). I should also point out I was wearing my glasses and had my eyes checked out about 9 months ago, so eyesight shouldn't be an issue
So, sitting up close to the screen, I can see what you mean, but this immediately looks like standard film grain to me - the silver wall texture you mention for freeze frame in chapter 7 is significantly out of focus (as are most of the backgrounds with noise on them) and I think this is why it looks like it's really bad noise if you're over examining it. Either way, I could barely discern much difference between the two players - if I had to choose one over the other, probably the S550 had a slightly better picture, but it's very, very close.
I then re-ran the comparison at my normal viewing distance of 9.5 - 10 feet and I have to say, only the fact that I'd just sat very close to the screen meant I could tell what you were talking about. The backgrounds where the noise are really just look like slightly out of focus backgrounds do in a film - I don't think this is a case of severe noise at all. The silver screen as mentioned, to me anyway, just looks like it's really out of focus (which it should really since Christian Bale's smirking mug is taking up most of the picture!!). Again, virtually nothing in it in terms of which has a better picture (incidentally though, I really noticed how much better the sound is out of the S550 which is not a comparision I'd run so far!).
Chapter 20 - why does this look so good? Very simply, this is one of the scenes filmed in the IMAX format - IMAX film has a much higher resolution than standard film (about 10 times apparently) so I'm not too surprised it shows up well! Have a look at
this comparison I've found which shows this quite well.
So, not sure if this helps other than the fact that, compared with a standalone player of about the same money, the PS3 holds up pretty well. Of course, there are better Blu-Ray players out there, and it might also be more apparent on a Full HD TV as well, but certainly nothing too wrong from my point of view.
Hope this helps