Ok, I've figured it out, it's simple to an extent but I'm going to post it here in case anyone else is curious or has this problem:
1. Open your epub in Calibre and, without changing any settings, convert it to either .lit or .mobi format (I found those to be the most accurate)
2. Take the .mobi or .lit you've created from the calibre library and copy it somewhere else and then delete the book from your calibre library list.
3. Now add the recently converted .mobi or .lit and have it convert to .epub format setting your parameters the way you want and after conversion, voila! Epub with no limited margins!
Maybe it's because the margins were fixed in the epub and the conversion to another format negates it but, it seems to work perfectly for me now. Thanks to all for the suggestions
