I was just looking over this and in fact Parker (An Introduction to the NEw Testament Manuscripts and Their Texts, for reference) and he mentions Collate. Collate is now in a second incarnation it seems but it was used on the NA28 apparently. It can handle a bunch of variant texts. There appear to be others like Quasillum's Perl script or Juxta Software's product. Accordance has something to compare texts which while not a collation is in principle not that far.
I hadn't actually been thinking of auto diff tools for this but was more wondering about data entry tools for manually constructed collations. That of course would be possible even using something as simple as a word processor macro.
Not being adequately familiar with the processes of text crit. I expect that there are many more specialized operations where more custom software is helpful., such as your own.