Cool looking mod. I have no experience making mods, but I can offer suggestions on what I as a player would prefer.
As for the quest, both sound promising. Though I suppose if you go through the old military facility the treasure could be an upgrade for alpha 115. That would explain where the new perk comes from.
Though like I said both sound interesting.
For the perk I would prefer that it not be something like making all robots non-hostile, in case you were considering that. That would be overpowered in my view. Maybe something that mildly increases alpha 115's firepower or armor. Though that might be too boring or mundane perhaps.
How about a stealth field affect that alpha 115 activates when you sneak, but which it has to deactivate and wait a second to divert power back to weapons before it can attack? I've never used the GECK, so I don't know how feasible that would be though I'm afraid.
Sorry if none of that was any help. Anyway, like I said, cool looking mod.