Yes and no. You can make it atomic if you check the entire repository (or at least the branches folder). However, it will not be automatic. You will have to apply the changes yourself to other branches. Different branches apparently have different code (you said that these are version branches), so applying the same fix to different branches may require different changes. You cannot (generally) always avoid human intervention.
I would challenge the idea of ββmaking everything look like 1 transaction. This will negatively affect the quality of your story. It seems that in many places you have changed your independence. If you merge with other branches a separate transaction, then the story will better reflect what you actually did (by making one change and porting it back). Is there a reason why you need to edit all branches in 1 transaction?
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