Once Quercus is established, people will want to migrate some or all of their business logic to Java code. That will present a problem for people who have non-Web-based PHP scripts (e.g. cron jobs or interactive shells) that need to make use of that business logic; there is no equivalent of the "php" command to run Quercus without a web container.
For example, my site has some database administration scripts that call our internal (PHP) APIs to ensure that our various caches get invalidated correctly. That would be ideal logic to move to Java code, but we don't want to have to rewrite all the administrative tools in Java as well.