How do I configure MySQL to accept a custom column in mysql.users?
YOU ABSOLUTELY, POSITIVELY, CANNOT DO THAT. Why ???
Back on Apr 12, 2012, I wrote the answer to Cannot GRANT privileges as root
I carefully explained how the grant columns existed from MySQL 4.x to 5.6. I have explained this many times (See my others).
The columns in the mysql.user table need to be in the exact position they are published along with the exact column names.
On Oct 10, 2014, I answered MySQL service stops after trying to grant privileges to a user where I gave an example of how you can hack repairs into mysql.user to comply with the next version.
I highly recommend you remove your custom column today !!! Otherwise, you will NEVER get all your grants back. Please go manage your database user identification in another database.