First, if you create a container database in 12c, Application Express will be installed common in the root container. You should never connect directly to a PDB, for any reason, and run a standard Application Express install script or patch script. About the only scripts that should ever be run directly against a PDB are apxconf.sql and apxchpwd.sql, both of which pertain only to configuring a single instance of Application Express.
Second, we have not released a new version of Application Express since Oracle Database 12c was released two days ago, so there is no software available to upgrade or patch the version of Application Express (4.2) that comes in the container database. The next version or patch of Application Express will contain the appropriate scripts to update a container database, so you are stuck with the version shipped with 12c until then. This seems to be contradicted by section 1.3,
"Upgrading to Application Express Release 4.2.1 or Later" in the "Oracle® Application Express Installation Guide Release 4.2 for Oracle Database 12c." It should be noted that the section currently only applies to non-container 12c databases.
My comments above apply only to container databases. Non-container 12c databases behave just like prior versions of Oracle, and you can patch Application Express to 4.2.1, or 4.2.2 as you normally would.
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