Need help merging unrelated histories

Everything I'm going to describe is related to this repository:

https://github.com/powervr-graphics/Native_SDK

This repo has several distinct branches. None of them seem to be tied to each other. Instead of having a `master` where they branched off each of their releases (e.g. 3.1, 3.2, 4.0), it looks like they made a copy of previous branches with no ancestry and then continued coding on that.

What I'm trying to do is go back and rebase all of the X.X branches onto a new `master` branch. I started off with this:

$ git checkout --orphan master

Then I committed a `.gitattributes`. Next, I rebased the first (oldest) release branch:

$ git rebase -i --onto master origin/3.0 --root

Then I merged:

$ git checkout master && git merge --no-ff -

Next, I did 3.1:

$ git rebase -i --onto master origin/3.0 origin/3.1 -X theirs

Using interactive mode, Git is smart enough to detect duplicate commits and eliminates those, even though the 2 branches do not share a merge base. I continued doing this all the way up to rebasing 4.3, but that's when things got tough. I see a lot of 'UD', 'UA', 'AU', 'AA' merge conflicts. These are obviously due to the fact that the branches aren't connected. But I expected was that `-X theirs` would always favor what's on the branch being rebased. However, it seems this only affects modified conflicts, not adds or deletes.

I was trying to find a way to bulk-resolve these. I mean, if git sees a file added on the left AND the right, I want the right one (theirs; the one coming from the 4.3 branch). Even though the branches are unrelated in terms of their history, I want the net effect of the rebase to essentially reflect the files on 4.3 itself. If a file isn't present on HEAD, delete it. If a file exists on REBASE_HEAD but not on HEAD, then add it. If the same file exists on both, favor the one on REBASE_HEAD.

But I don't see a way of doing that. I tried `git checkout --theirs .` and `git checkout REBASE_HEAD -- .` but this doesn't work with all conflict types.

Can anyone provide some advice on how to properly restructure this repository to create some ancestry, as if all along a `master` existed and all release branches were based on this in a linear fashion?