Hi There
While I'm not entirely familiar with how things work on the SellerDeck end - you can I believe have one WordPress install in the root and have different sections like /blog and /help etc - but put other non-wordpress things in /store or any other folder you want. So long as you don't try to make a page, post, category, tag, etc at /store you should be good to go. FYI two WordPress installs shouldn't affect speed but it may be more of a management and consistency concern, but I don't think you need to do that.
I am not totally sure I get the bonus question In this scenario, the ecommerce platform would serve the homepage? What would WordPress be doing in this situation? Thanks for clarifying and I'll try to help out!
-Dan