Quick work-around:
Extract the PHAR and rename the files. This way your application still works, and phpstorm doesn't choke on the PHAR.
php -r '$phar = new Phar("vendor/phpstan/phpstan/phpstan.phar"); $phar->extractTo("vendor/phpstan/phpstan/phpstan.tmp");'
rm vendor/phpstan/phpstan/{phpstan,phpstan.phar}
mv vendor/phpstan/phpstan/{phpstan.tmp,phpstan}
// See original answer in https://youtrack.jetbrains.com/issue/WI-57899#focus=Comments-27-4656373.0-0