So I've found that there were 3 community patches for this game - version 1.02 build 44, 45 and 46. I'm assuming the GOG version does NOT have those applied? I was able to download them and install them, but at that point in then starts asking for a cd to be in the disk drive to play, so that makes that not work. Also, you can download a no cd patch but that doesn't run in windows 7. So basically are we stuck using the actual retail version? Or is this patched to build 46? (which is unlikely)

I understand your confusion given GOG's policy of only using "official" patches. But in this case they found a way to get around that. Maybe they got official permission. I don't really know. But the GOG version does contain those 3 patches, builds 44, 45 & 46.
So you have no need to apply any patches and then you won't have the cd check problem.

edit: You'll notice that the GOG install contains the GCT setup application. That comes from the build 46 patch.