I am not so sure about that. As in one of my sites in the root I use an index.php file that redirects the customer to the cart. I only have around 2000 products and google has 4040 links to my site they have both the php version indexed as well as the catalog/html version. It is more of a penalty if you redirect your customer from your domain to another domain and are just using a site as a doorway to your other site. As long as it is staying in the same url it appears you are fine. At least with my 60 websites I have never had a problem with it. Just my opinion though I could be wrong but as said I do not seem to have been penalized for it and have been doing it for a couple of years now.
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