Keeping links to internal .php pages

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Does setting up More URL's under Page Paths and Location in page properties such as home.php (plz note the .php extension, as c5 generated pages does not end up in an extension rather in a directory) actually create two URL's for same page.

If yes, it definitely bad for SEO. How to mitigate the problem if you are moving an HTML site to c5 and have pages (that ends in .php) being linked to or ranking for keywords in Search Engines.

Kindly first clarify whether setting up as above does create 2 URL for same page and suggest an alternative method other than setting up 301's in .htaccess.

Moreover If I link to internal site page with something as below:

<a href="<?php echo $this->url(''); ?>about-us.php">About Us</p>

would that be SEO friendly

Basically, I would like to keep .php extension(setup as additional URL's) links to internal pages, is there an SEO friendly way of doing it.