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At a fundamental level, you are keeping the data somewhere and it is rendered correctly. In a CMS this data is stored in a database completely outside search engine view. So it does not matter if it is in database or in physical directory somehow. So there is no benefit in keeping the structure same physically. Having said that and my own experience (we manage website with millions of pages) managing this using HTACCESS script is NOT a good idea. You will be limited by what you can do and maintaining will be quite challenging. I strongly suggest consider moving to a CMS (like drupal) and store all you content inside a database and the CMS script takes care of HTACCESS plus gives other goodies. There are several tool available to get your content from disk into a database.

You are assuming correctly. The spider will see the content that is shown by default, which in your case should be the retail pricing.

I would expect if he used the redirect domain function in google webmaster tools it would minimise this.