RunSingleJob.php sets $wgCommandLineMode only after an exception was thrown:
https://gerrit.wikimedia.org/g/operations/mediawiki-config/+/e673cccabc288368b4dc52e937794660f600606e/rpc/RunSingleJob.php#97
This is documented with "Since output is logged to file, get MediaWiki to generate a raw error". This would make a bit of sense, but the output is not actually logged to file, as far as I can tell. I can't find any such logging in the code calling RunSingleJob.php (actually, I can't find the code calling it, it's all YAML definitions, but they don't mention logging: https://codesearch.wmcloud.org/search/?q=RunSingleJob.php), and I can't find any evidence of it in Logstash (we have plenty of exceptions logged from RunSingleJob.php itself: https://logstash.wikimedia.org/goto/d0c91bdf2f6079dc24a0ae7633fd976a but when I try to search for these error messages and exclude it, I find nothing).
So the command-line-style output is either unused, or it's so cleverly hidden that I can't find it. Let's try removing it, and see if anyone complains.