I use your mental damage rule at my table. My players disliked being stunlocked pretty badly, so I make the rune go through wounds before another rune gets damage applied to it.
I’d be careful with your passive power build with high destiny dwellers. Perhaps makes it focus-like, in the that it is applied after runes. As it is now, it might stack with the extra rune they are getting from being a high destiny character.
I don’t see a serious issue with your cinematic interpretation.
The in combat rules are there to simulate being able to accomplish great deeds in combat because of an adrenaline rush (asked about this myself some time ago). No reason you can’t make them the same system (or change the system complete, as I did).
With your stacking of metas, #1 can be summed up by saying that they only affect a single source (which is the single numeric you mention). That won’t do anything for powers that are simple (power attack, backstab) rather than house that are complex. Most of the powers are balanced mathematically on the back end, so putting in this distinction actually may cause you a problem.
In your second option, that won’t be an issue until after destiny 4 (rune, meta, meta, meta, then a void rune as a meta). I suspect it won’t cause a big deal, but it will probably be less fun for the players
