I'm looking at specifying multiple containers for a task via this tutorial: https://docs.flyte.org/projects/cookbook/en/latest/auto/integrations/kubernetes/pod/pod.html#multiple-containers , however, I'd like to change the env variables to a pod based on inputs to the workflow. Is there a way to dynamically change the pod env variables?

you could use dynamic workflow. create the pod spec based on the inputs. https://docs.flyte.org/projects/cookbook/en/latest/auto/core/control_flow/dynamics.html#sphx-glr-auto-core-control-flow-dynamics-py