@jonhattan, that is an impressive test. I didn't measure time precisely but I can tell for url_alias migration which contains 30k entries, it took about 40 minutes to run before the patch and about 30 seconds with the patch. The file migration where I saw the 6000s query had 300k entries and never finished. It took an unreasonable amount of time even after I increased join_buffer_size to 32M. Personally, I would discard the very long times for url_alias and file migrations from before because it could have been a misconfigured MySQL. I have since tuned the config using the MySQL tuner script.
I can try repeating the migration without the patch a bit later. I am focused on completing the migration right now. However, your results show a 5-18% gain and that is not small.