I would definitely say that you must configure MySQL to work on a different EBS volume for many reasons. Here are a few:
Easier backup. You can take a snapshot of the entire volume of EBS, instead of dumping MySQL and pushing it to S3. When you have a snapshot of the volume, you can restore your database much faster than with a MySQL dump.
. , . , MySQL. MySQL, Data .
EBS .
, .
. , .
, EBS, , NOSql, Amazon RDS .. , MySQL , .