I've had trouble accessing .pl files on some of my sites when using Internet Explorer from a machine that had perl installed on it. The browser would occassionally try to execute whatever was returned by the CGI program because it thinks .pl means a perl program so it tries to run it. When I run into this, I rename them to .cgi. This allows me to figure out what the real problem is without the browser getting in the way (Windows doesn't know what a .cgi file is). All I have to do is put a little directive in my .htaccess file to tell the web server that .cgi files should be processed with perl.
If you wanted to, you could modify your own web server's configuration files to change the file extension mappings. You could write your web site in perl using files with .php extensions so long as the web server thinks .php files should be processed with perl. You could also write your web site in php with .pl extensions so long as you tell your web server to process .pl files with the php interpreter. It really doesn't matter what the extension is so long as the web server knows how to map it to the right processor.
I'll agree with the first reply in that none of this should matter at all to search engines unless they are trying to guess what language your site is written in.
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