Yes. You can do that. But I would recommend spending a bit more time to move to separate web and data containers so that you have only a single instance of redis and Postgres running. But if you don’t care about wasting some ram and don’t need the benefit of reduced down time when your rebuild, your idea is fine.
This will use a bit more ram than a multisite setup but allows you to have different sets of plugins.
In that case, yes, a second copy of samples/standalone.yml will do fine - but: make sure to update the /var/discourse/shared/[standalone]/ and other host-exposed resources to another name.