The title says all,
I would like an option to be added in the SQL config in order to have different MySQL tables, so that, I can run different stats on my BungeeCord network,

Thanks in advance

What do you think about a configurable prefix?

I know the table name in MySQL is: player_stats
Do you mean a new config option (Tableprefix) in sql.yml like this:
SQL-Settings:
Tableprefix: 'prefix_'
Username: awesome_user
Password: awesome_password
Isolation: SERIALIZABLE
Driver: com.mysql.jdbc.Driver
Url: jdbc:mysql://localhost:3306/awesome_database
Timeout: 1000
uuidUse: true

The new table name will be: prefix_player_stats, and this value, by default, an empty string.
If so: All of my YES! :D