No; PHP is run once per script, and the whole file (and any included files) is passed through it in one go, HTML and all.
The only difference is that the PHP parser doesn't try and interpret the HTML as PHP code; but then, it doesn't do that when it's reading a 'single-quoted string' either, so that's no big deal. It does have to be a bit more careful with "double-quoted strings", 'cos then it has to look out for interpolated variables. Again, though, the compiler sorts all that out before script execution, so the difference is negligible. From experimental timings I've seen the difference is on the order of a millisecond or so.
PHP has to read the entire file regardless of how many or how few <?php ?> groups there are, for the simple reason that it has to find the <?php ?> groups anyway.
If you're really interested, you can dig through the source code!