Marketpress in homepage (subdirectory install), without slug


I want to install marketpress in a new wordpress install that would be created in a subdirectory. That is, I have with a wordpress install, and I'm planning to create another new Wordpress install in a subdirectory (store, for example) in which will run Marketpress.

The problem, is that in Marketpress you need to enter a store base slug (let's say "shop"), so the final URL would be something like for the store base, and for a product.

What I want is to have a URL like for the store base, but having marketpres (in a new clean install) installed in the "store" subdirectory. That is, no slug for store base. My problem is that the Wordpress install in the root directory is a huge one, with more than 20.000 users (and I want to keep both sites separated for performance purposes), and I'm also planning to have different themes for the main site and for the store.

Is it possible? How can I make it work?