Phar supports zip, and zip files can be password protected. But you will need a monkey to enter the zip password whenever the request comes. Therefore, no, not useful for closed source software.
But to make this a somewhat serious answer, no, it really doesn't work:
PHP Warning: include (phar: //phar.zip): stream could not be opened: phar error: Cannot process encrypted zip files in zip-phar phar phar.zip in php shell code in line 1
mario
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