Doesn't answer your question, but I use Winmerge with some tweaks to the settings to make the highlighting a little nicer:
http://forums.winmerge.org/viewtopic.php?f=4&t=1040
If I need to compare 1000s of messages from two sets of transforms, I then point their outbound to a single fileout (or since I upgraded to 2019.1, using the export) and then compare the two files.
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