Ah, if the chroma subsampling is changed that would explain a lot. I did take a look at the "cleaned" file and the JPG quality was also lowered from 99 to 75 meaning it was recompressed as well. Comparing them side-by-side the smaller version is slightly grainier and has some minor JPG artifacts. Whether that's a big deal is up to personal preference. The images could definitely be compressed a bit more compared to the original without affecting the quality at all, but the cleaned version is slightly too aggressive in cutting file size IMO.
Anyway enough nerd talk, let's get back to gooning shall we?