None of these solutions work because the callback functions for rules are only called on module enable. hook_rules_config_execute() does not allow you to modify the config, it just provides it so that you could know those settings for whatever else you are doing. Thank you for taking the time try to answer the question, but it doesn't work.

When you are speaking of the rule's callback function, what exactly do you mean? Do you mean these drupalcontrib.org/api/search/7/hook_rules? None of these callback functions would work from what I can tell. hook_rules_config_execute does not give a reference to the config, so no changes can be made to it that would effect the original rule.

Did you ever find a clean solution to the problem that was a tool for doing this?

Ultimately what I did was create a Basic page with the url alias store. I made sure that the product catalog and the shopping cart showed up on that page by adding store* to the pages that those blocks were to show up on. I then changed the front page to be another content page. I was then able to access the store via <mywebsite>/store. This is very similar to what you suggested so I will accept your answer.