Just a few thoughts as someone who has done a bit of bibliographic work. First of all, Hinman collators are a migraine waiting to happen!
I've only used one once, since there are rarely two or more copies of an early modern handpress book in the same place (except of course for Hinman's work on the Shakespeare First Folio at the Folger which owns way too many copies!). It was exhausting on the eyes.
I like to bring a copy of my own with me to a library (usually printed to scale from a microfilm or an online source after running it through scantailor, which is a lot easier than doing it with imagemagick!) If I can afford it, I try to print a to-scale set on transparencies. Then I can just put it on top - if there is a blur, there is a discrepancy.
When doing digital collation, I make binarized images and scale them to size. (Scantailor has made that easier) I then choose one to use as the copy that I always compare others to. The others I convert to transparent images. Instead of alternation, I just use two layers in Gimp. A straight overlay doesn't do things perfectly, since pages have shrunk differently over time, so I just move the transparent image around. When there is a blur, it means that there is a difference. It's the fastest way I have managed so far. I figure it takes about two or three minutes to compare two pages, including setup time. I wish I had the rights to share some of these images with you. If there is an interest, I can try to get a letter of permission to show a page from two libraries. (might not happen though)
It is a lot of fun to figure out the editing process of a hand press book. It's necessary too! Books printed by hand will always be unique. Each copy will be a mix of corrected and uncorrected pages. How do we know what a document says if we don't know how the document was made? There is nothing worse than a hardcore textual critic thinking that the use of a semi-colon or a colon in a poetic line is always significant. Printers made mistakes after all. The only way to know if a small detail is important is if someone took the time to change it. Pure analytic bibliography can also be taken too far... (classic example
pointing out how ridiculous it can sometimes become)
So, in summary - alternating gifs are a lot more difficult to deal with than just compositing two images together.