When the EN$TRITE DD statement is added to turn on the IF/THEN/ELSE trace, the trace output is embedded in with the Processor C1MSGS1 output and not written to a file defined in the EN$TRITE DD statement.
Can the CA Endevor IF/THEN/ELSE trace output be directed to a separate dataset?
No. If you want the EN$TRITE output separated from the Processor C1MSGS1 output, you can do it in a post execution processing step.
Direct the C1MSGS1 output to a data set and then use SORT or ISPF X ALL / F C1X0000I ALL, to separate out the EN$TRITE C1X0000I message lines.