I suspect this is something you'll have to keep using mods for. While I agree these things should be options, I suspect the devs intentionally chose to leave them out so that dying would be more punishing, as part of their "vision" for the game.

IMO, skill loss on death should be adjustable, not just for people that want it lower, but also for the masochists that want it higher. Some people play permadeath runs, so I'm sure there's a number of people who would like to see a difficulty between that and the default 5% skill loss.