I guess it makes sense that if it replaced the original DNGs, it had no file to copy EXIF data from anymore. Luckily, I was able to rename all of the IMG_1234-dualiso.DNG files back to IMG_1234.DNG that were still in Lightroom's library and have it write metadata back into the files, so nothing was lost.
Ah, I was sure the sticky post had the newest version. OK, I'm now on BETA3.3 and it doesn't overwrite IMG_1234.DNG anymore (though it says in the .txt logs that it copies EXIF metadata from "IMG_1234-dualiso.dn6", which is the suffixed name with a number six replacing the last character, for some reason). And, EXIFs are present, correctly.
EDIT: Oh. This newest version converts everything even if no striping is detected, creating -dualiso suffixed exact copies of source files. How do I get it to ignore non-dual source files..? I used to be able to just select a whole folder of photos and let the plugin do the work, converting only striped images...