They do not share a file format. If you look at the GitHub repo for this site (https://github.com/magcius/noclip.website) you will find parsers, etc. for every single game.
Are you reffering to the graphical butchering that occurred in the gearbox port? I grew up playing CE on the PC so if wasn't until years later that I found out how much I was missing graphically compared to the original.
I originally only had CE on the Xbox, and I later played CE on the PC. I always remembered the Xbox graphics being better and I chalked it up to a nostalgic view of one of my favourite games.
I've been a huge Halo fan and played all the games and it was only last month I learned that the gearbox port genuinely butchered the graphics.
2. Are they converting the extracted maps to some common format, for which there's a JS renderer?