It's a simple sum. You should calculate the website quota and then sum the mysql database size to it.
Linux filesystem quota is enforced by a linux kernel module, it is not enforced by ispconfig like traffic quota. ISPConfig just sets the quota values with the linux quota tools for the filesystem. So you would have to extend or write a new linux kernel module when you want that the file system quota takes mysql quota in account when it should block file access when the mysql database exceeds a limit.
If you would sum it up as you said, you can block access to mysql of yourse when the sum of disk plus mysql quota is exceeded, but the client will be able to create more files on the harddik until the disk quota recahes the overall quota. So the max value in your setup qould be mysql size at the timepoint where the sum of quotas exceeded the overallquota plus the complete sum of the overall quota as disk size. So even if you sum it up, the client can take more space. So its a cleaner approach to have a defined disk limit and a defined mysql limit also disk space is normally "cheaper" then mysql space as you often run mysql servers on ssd's while you use a traditional harddisk for website space and processing of large databases costs a lot more processing power. So mixing a expensive storage space and a cheap storage space in the same limit is not a good choice.