Hi,
My main concern would be SEO rankings - especially when the word is the same (just the meaning is different!)
Couple of comments...
As I see it, for SEO reasons it really only makes sense for one store to use two "Parent Categories", rather than two homepages... which still means one homepage.
Logic being that every PAGE can only be indexed for 1 really (or 2 if lucky) main keywords and I am not sure how you would reflect two homepages to have equal SEO weighting or even have two homepages really!!!
As essentially no matter how you set things up whichever content is used on the
www.domainname.com/ page will be seen to be the domain website's "homepage" (main site page) for SEO as I understand it.
So I would consider a custom homepage with two link options on it - a link to "parent category 1" and a link to "parent category 2".
Outside of this, if they really must be separate main words, which deserve separate websites... then do that and run two separate sites on two different domain names / two different IP addresses (the easy way to do that as you know would be to use two copies of X-Cart / 2 separate stores to do that).
I hope my comments do help to some degree
Cheers, Asiaplay