I don't think the difference is deliberate exactly, but it wasn't one of my goals to do exactly what a Calibre conversion does either, for example it also won't modify every flow unless Calibre (or someone else) had done it previously. I do recall wondering why Calibre conversions use body for left/right instead of just using @page for everything. I know Calibre doesn't use body for top and bottom margins because that will only apply to the first and last page of a flow.
it's been a long time since I messed with this so I'd have to review the code in detail to answer this question fully. I don't think you'd get double margins from the plugin as it modifies both page and body margins - i.e. margins in body should be removed and everything would be in @page. It does sound like you're saying there may be an edge case if you run the plugin and then follow that by running a Calibre conversion. Calibre might insert the margins in the body tag whilst leaving @page alone, not sure of this, but since the whole point of the plugin is to avoid a Calibre conversion I'm not sure how critical it is. I sort of doubt this is an issue anyway as it could potentially happen with any number of retail ePubs as well and I haven't heard of Calibre doing that.
Edit:
Looks like I summarized the work I did fairly well here:
https://www.mobileread.com/forums/sho...&postcount=144