Really they should just be separate repositories (because as you say, they are independent code bases), but I think if you want to force them to be in the same

Really they should just be separate repositories (because as you say, they are independent code bases), but I think if you want to force them to be in the same repository, they should at least be on different commits that are tagged instead of what they're currently doing. Whether or not you decide to base the commits on each other is something else that can be considered. If you really don't want the commits to be based on each other, you can just make new orphan branches.