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The great thing about RDS is that it's a managed service. This means that under the shared responsibility model AWS takes care of all management tasks for the DBMS leaving the customer responsible for optimising the application to suit their needs.
In your case, the downside of this amount of AWS control is a limitation of the commands that can be executed. You have the ability to perform high level "standard tasks" (naming DB, Tables, Indexes, Procedures, etc) but loose control of the underlying OS and file management.
I fully understand that some people require/insist on having full control over their DBMS and in these situations you would probably have to look at running your DBMS directly on an EC2 instance, however, I strongly advise weighing up the pros/cons for realising this functionality. Especially the extra costs that can come with appropriate instance types/block storage/networking.
I sleep very well at night no longer having to worry about managing replication/backups/uptime/etc as all of that is taken care of by AWS.
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