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Modify ePub does *exactly* the same as calibre does when converting when it comes to sizing covers. I would suggest you have been fiddling with your calibre defaults, and the reason why you see a difference is because you are testing it on a book with a saved profile with your old settings on it.
If you are talking about white space left/right then that sounds like you have been changing your "preserve cover aspect ratio" setting in Preferences -> Output Options -> EPUB Output. The only other sizing setting relevant to covers is mentioned above of the default device you have configured, which is in Preferences -> Common Options -> Page Setup.
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