I’m having the exact same issue. MySQL 5.6 to the MySQL 8 (MariaDB). I’m using the latest version of SQLyog. I’ve tried both to copy and sync. Both fail. It’s the sync tool that shows the definition match error. Doing a copy just spins along and says all is fine, but it really not. When it’s done I have no data in my target DB.
I just paid to update my version of SQLyog expecting it would be able to do this for our migration from one hosting provider to another. If there isn’t a work-around, SQLyog is useless to us.