Have you been able to solve this problem? I have exactly the same problem when trying to upgrade the Apex version in the 12cR1 container database to version 4.2.3 with the patch set.
I installed the patch without problems by executing the SQL scripts in apxpatch_con.sql line by line in SQL*Plus, ignoring the catcon.pl perl script lines.
I cannot vouch for the specific error that is being returned by catcon.pl, but I would try the following in your situation.
1. It seems you connect to CDB$ROOT and ran apxremov.sql. This only removed the common APEX option from CDB$ROOT. Your PDB is now in an inconsistent state, since APEX is no longer in the root. I would reconnect to CDB$ROOT and run apxremov_con.sql, make sure you use the one from the 4.2.3 distribution. The one in the ORACLE home will not work.
2. I would then re-run apexins_con.sql connect to CDB$ROOT. Also, you need to pass the proper parameters. Why are you passing i10wrk? You should be invoking it like:
@apexins_con.sql SYSAUX SYSAUX TEMP /i/
I had the same error messages when trying to apply the 4.2.4 patch to my CDB.
For some reason the environment variable ORACLE_SID was set to "cdb1" by the installationscript of 12c.
After changing it to the actual name of my cdb (default is "orcl") the patch runs fine.