No. In terms of io and other kinds of overhead, you are always better off running your database on a container rather than a VM. The majority of public cloud database services are either running inside containers, or in the process of migrating to containers.

An additional advantage of containers is that you can start running them on top of a VM, and then migrate to bare metal later, as your infrastructure requirements evolve.

I think in my head I had container ON A VM. Which just inherits the problem of running it on a VM. Is there a good linux tool for limiting the IO of a process or user?

Networking uses tc and disk uses the block I/O controller. https://www.kernel.org/doc/Documentation/cgroups/blkio-contr...