Hello,
ttansactional metadata queries should be able to find these nodes as those queries operate on the DB where the index control aspect is not evaluated (as of 4.2.4). Have you made sure that your queries are actually being executed against the DB, i.e. is the metadata indexes patch applied to the DB and your query consistency set to "transactional only"? I have been fooled myself a number of times (before getting it) when the query "appeared" to be executed against the DB but in fact was still running against SOLR.
Regards
Axel