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As mentionned in the subject of this bug, EGit is creating its own custom implementation of the TypedElement interface when using the "right-click > Compare with Version in Ancestor" action from the commit viewer on a changed file (bottom right of the history view). This means that the files will _always_ be compared as text instead of using the proper comparison engine, effectively disabling tools such as EMF Compare (that provides custom comparison engines for EMF models). Furthermore, this does not make use of the ModelProviders in order to determine whether the "changed file" is part of a logical model before comparing it. This second issue makes this bug a blocker for bug 354474.
I suspect the same underlying problem as with bug 354923 and cannot reproduce with the described steps.
Benjamin, see my bug 354923, comment 2 ; This issue seems fixed on master.
Great!