Different readers may have different settings. Some let you change the default margins on the fly, some have fixed rather large margins you cannot change.
Then, Calibre has many settings too, some of them may be affecting the relative dimensions of the images, or how they are interpreted.
Additionally, the comics you bought may have been in "fixed layout" format, which is something contrived by Apple that as far as I know is only understood by iBooks and does not conform the ePub spec, at least not version 2.0.1 (I believe there's something about it in ePub 3, but I don't know if it's the same as Apple's).
Anyway, wouldn't it be easier to install a comic-reading app in you iPad?