Sorry about that, should be fixed now!

Correct, until you click the "download" button from the bundle page the game will not show up in your library or that your account owns it.
The collections are more for organization/browsing through the contents. There are filtering options in the Itch.io app, but it doesn't make any distinction between TTRPGs and video games for example. Both are lumped in under "game". 
There should be a search bar on the bundle page that allows you to find the specific item you're looking for and download it from there. A bit roundabout, unfortunately, but that's currently the easiest way I'm aware of.
Alternatively, you can take 45 mins or so and Ctrl+click every single download link and just add everything to your library like I did, but I can't say that's a pleasant experience. :P I saw some scripts floating around the internet to auto-add everything but I couldn't get any to work and I think it was asked not to use bot scripts anyways. 

Slow reply on my part but thanks! I'll try to get it updated within the next day or two. I don't own VR equipment so I knew it was possible I didn't know what I was looking for and missed some things.

Yes, the final bundle count was over 1700. While I didn't update the original post with the final number, I did updated the collections themselves and they should include every single item from the bundle.