On your first question I would rather it stayed out of the lobby, and I say that as someone who argued for a different setup option in another thread here a couple of weeks ago.
The difference, for me, is who a setting changes the game for. A choice that affects only my own machine costs nobody anything. Health, shields and damage are not that. Once those are adjustable at setup, every game starts with a negotiation about which numbers we are using, and in most lobbies the honest answer to that negotiation is whatever the host prefers.
A mod at least announces itself. Everyone installs the same thing and knows they have done it. A slider sitting in the lobby looks like an option rather than a different game, which is how people end up agreeing to something they have not understood.
Single player I would not argue with at all. If someone wants to raise their own shields while they work out what the Eidolon are doing to them, that harms nobody, and it is a smaller request than the lobby version would turn into.