Checkout official (`git checkout official`). Now, switch to a temporary branch (`git checkout -b tmp`). Make your changes. Check that everything works. Commit the changes (`git add ...; git commit -m "..."`). Tag it (`git tag shader.ppr.0`). Then checkout arc3.master and merge in your tag (`git checkout arc3.master; git merge shader.ppr.0`). (At this point the temporary branch can be deleted.)
That's the simple way to do it, anyway. You can in fact make changes which are "relative to" official even if you actually do the work in a temporary branch derived from arc3.master, by using git rebase or git cherry-pick, and I'd highly recommend learning how to use these and other advanced git commands. Also, if you want or need other hacks, you can merge them in after switching to a temporary branch but before making your changes.
And yes, the arc3.master branch does contain all the changes in the arc3.help branch; whenever I change the help branch I merge it into the master branch as well. Note, however, that the reverse is not true - the help branch contains only the modifications needed to get the help system working, and not the other changes in the arc3.master branch.
Does git not check out tags unless they are requested? Otherwise wouldn't all of those changes stay on the official branch as well? Though I suppose the official branch won't be pushed to by most people, it would still clutter the local version, wouldn't it?