Its because he is using 1.4.0.0 UI.X on XenForo 1.3.5. XenForo is going to flag the templates as outdated as technically the UI.X. templates are ahead of the master templates.That's odd. Maybe its just with drift. I installed the UI.X update on 1.3.5 and have no templates to merge.
Hence I would just use the corresponding version of UI.X with that of XenForo or one less.
Another thing to note, just in general, and you can quote me on this. In 99% of 'merge' situations nothing significant is going on so you don't always NEED to merge. If its header/page_container/footer or navigation related, I would say that is important. The rest, really is not that big of a deal, generally XenForo is fixing inconsistencies with RTL, languages, screen readers, html standards, etc. So if you are the average forum you won't need to always have up to date templates.
ALL that said, it really shouldn't be that complicated to stay up to date either. The merge center should handle 75% or more of all situations. The rest of the templates, just leave to me and an update if you aren't comfortable.

