Do I understand that 1) mail in queue can be delivered, but fail to get removed from mysql tables?
Yes, records in SQL db won't be removed automatically. but iRedAdmin-Pro provides a script (iRedAdmin-Pro-x.y.z/tools/cleanup_amavisd_db.py) to help you remove old records.
2) removing the messages via the script does no harm with respect to msgs in the mail queue?
Yes, records in Amavisd SQL db is just a log, not real email messages.
I have read and ran the script, but again, nowhere do I find a clear explanation of how these tables do or do not relate to the mail queue leaving room for confusion.
This records were inserted by Amavisd, used to help track in/out emails, but they're not real email messages like the ones in Postfix mail queues (/var/spool/postfix/). You can delete records in Amavisd SQL db anytime you want, but please don't delete messages in Postfix mail queues.