brookman, is it possible to turn off crop altogether? See the attached images; I haven't tried v1.1 but I don't think it would catch this.
Kolenka, I like the idea of keeping a single version, but good scans have big file sizes (1+ MB for covers, 200-300KB for pages). Page turns for these are ~1 second as opposed to ~1/2 second for manga2cbz processed images. Plus, I go in and delete scanlation group credit pages, because these days I'm embarrassed to show a comic only to come across a pages that says: "TFT. We Love Beavers."

That shoots the single version idea in the foot right there.