You are far from alone!
Indeed it is, When you download “latest” or any other tagged point in time, you are downloading the whole caboodle and you can switch between the branches.
Yep, the default branch name when there is only one branch is master, when you start adding branches, the default branch you see when going to GitHub or when you clone/download without specifying a branch is “master”. The master branch is usually considered the “main” branch if you like. But emoncms not only calls it’s main branch “stable” (which is a little presumptuous) it also calls it’s secondary (development) branch “master”, which although perfectly workable when you know about it, isn’t as obvious as it could be.
Calling one branch “dev” or “development” is crystal clear, as for a “released” production branch, “released” is clearer but “master” maybe more expected, I think I prefer “released” just to avoid any preconceived idea’s about what “master” might or might not be, but all that is really important is that it is clear and consistent.