The Github projects are a very small part of the open source universe. You can easily build *BSD or LinuxFromScratch with a substantial userland without ever downloading anything from Github.
To your second point, you're right. I'd love to be able to convince older OS projects to move to GitHub. Some do, but it's an uphill battle.
Yes, other websites show source inline, but I've found that they are not intuitive at all, and the code (to me) feels hidden.