Hey Craig,
Yeah, per container env variables are fine; if you want to have lots of containers that all have a slightly different setting for the env variable, you'll want to use the "containers" arg in the yarn configuration instead of the "container" arg, where "containers" is an array of tables, one for each kind of container you want to launch. The "container" arg is a shorthand for the situation where all of your containers for an application are configured the same way.
I hope that made sense. :)
J