How can I ensure that the inputs do not become 'twisted' after making the Supermodule, e.g. Left input becomes below Right in a stereo input/output SM?
The solution is eternal vigilance.
How to give names to inputs/outputs of the Supermodule?
You can't really. They retain the names of their underlying connections. You could try using a NODE module (C-C or A-A) to "decouple" them.