Well, few reasons I think that Issac isn't able to see inside the temple. First off is they way he responding. He didn't just say "That's fascinating", he said "Hmm. Well. Isn't that fascinating..." This, to me, sounds like the sort of response you might give when you have your 'see through stuff' power blocked, as opposed to seeing something that is actually surprising because of it. Another reason is more of an artistic thing, in that his 'see through stuff vision cone' is stopped by the pyramid as it is drawn. Generally, though not exclusively, when drawing something like that the 'colored vision cone' would allow the viewer to at least partially see through whatever is being seen through. Instead it remains 100% solid for us. Finally, he does this -before- we see the shot of Parson about to carry some bodies through the portal, indicating that he likely said that before any bodies were present. Now, it could still be fascinating based on the design of the building itself or something, but it likely isn't because he saw bodies.
Even with all that though, I'm still only about 60/40 as to if he can actually see through it. I'm more interested at the question of if Sizemore can actually make a building that Issac can't see through. Also keep in mind that he seems to be using lookamancy, not thinkamancy, which may have different requirements to block than the more stringent ones of thinkamancy (think lead as opposed to adamantite in most fantasy settings).
Alright, as for the 'stuff is stuff' debate:
Dittomancy is numbers aligned matter (aka stuff) magic and has been shown to duplicate not only arrows, but Units as well. It has also been stated that it can duplicate other spells (indicating possible proof of an E=m*c*c conversion). Also, and this might be the most important to the current discussion, it can duplicate magic items to some degree. The clone of Slately was duplicated with magic items. The jetpack is shown to continue working, as was the foolamancy blocking ability of the magic crown, and the magic blaster. All of which were magic items created by a dollamancer (except the crown, that was created by a hatamancer). Also, the main place I'm drawing the 'stuff is stuff' thing from isn't from a stuffamancer at all. Olive and Wanda use that during their meeting, in which they talk about people, plants, corpses, and uncroaked, all just being 'stuff', and the only difference between them being the presence of life and/or motion.
And of course there is Sizemore creating the wooden support beams (which are about as much like dirt as flesh is from a real world perspective) from dirt when making his tunnel. He also made, though it hasn't really been brought up, some kind of lights. They could just be those little power orbs that we've seen floating around fairly regularly, but they look alot more like small gas lamp or something to me since they look attached to the wall as opposed to simply floating there. And if that is the case, he created a whole slew of things out of dirt.
Also keep in mind that the temple and the devices surrounding it are said to be made of thinkamancy-charged stuff, which seems to show even further that stuff is stuff, since they aren't made out of thinkamancy charged rocks, or metal, or wood, or anything, just a very generic 'stuff'. Now that said, I do have to agree that the thinkamancy-charged part is likely something that sizemore couldn't do without help from maggie, but I'll direct you back to above: He is (potentially) blocking lookamancy, not thinkamancy, which may be easier to block, just like it is easier to block x-rays than it is to block radio waves (well, maybe not easier, so much as different). Sure, you may need thinkamancy charged stuff to block thinkamancy, but you might just need lead or something similar to block lookamancy, and Sizemore can almost certainly create that.