Unfortunately, it seems the add-on isn't going to do what I need it to without the use of alt IDs, which is impossible due to the number of combinations that would be necessary. I wish I'd known that before plunking down £49, but I'll do with it what I can.
Update! I've fixed some of the problems I was having with this, and currently have it enabled. The one thing I can't figure out is why my thumbnails are displaying in two columns instead of one row. I haven't changed any of the settings. I don't really like having two columns when there are multiple images; it looks really awkward on the desktop site. For example: http://www.sleepingbaby.net/proddetail.php?prod=wrapsody Is it the size of the image it starts with that controls the way the thumbs are displayed? I can't find anything on the MagicZoom site that explains this, and all the demos just have one row, not two columns.
which means there is only space for two adjacent thumbnails - if you increase that there will be space for them to go on one line. The hover and zoom worked fine for me there.