Yep, the close-ups occur within long CGI shots - and besides, Muren tells us they're CGI close-ups. Toward the end of post-production he really wanted to see how close in on a CG dino he could get without it falling apart, and tried it - totally successfully - in that rotunda sequence. Earlier in the film we had gone fairly close in on some of the Brachiosaur skin, but that looked less photographic to me - gorgeous, though, like a moving painting. But the final Tyrannosaur close-ups were something else.
Still, the confusion between animatronic and CGI in JP is great. On the whole, I spotted Winston's stuff from ILM's, but there was a Winston shot which I took for cgi at the time - the standing raptor that forces them onto the skeleton display.