As Installer said, there are probably some resources that are being saved when not using PHP extensions versus PHP extensions without any PHP code.
The question is, should we care? Probalby not.
A PHP script I created which scans a 114KB data file using Perl's REGEXP syntax (3 different intricate REGEXP's), some parsing, some date/number formatting, and outputting, takes only 0.0085471 seconds to load.
So, if a PHP script using all of that can load in 0.0085471 seconds, a PHP script which does nothing but transparently pass the data on to the output stream probably takes 0.0000001 seconds to parse.
So, if you use a .php extension with NO PHP code, then yeah, you're probably losing 0.0000001 seconds! 😉