As far as comprehensive safezones not hurting warbase paradigm: I can already see 2 ways:
Without a hard shell system, you cannot prevent people from entering your airspace and gathering intel about you and your station. Sure, you can attempt to kill them, but an extremely speedy flyby that drops off 5 endos will be almost impossible to stop, and they will be able to gather all the intel they want. All warfare is based on deception, and you if you can't prevent info, that's a significant 'hurt'. Only your station is safe, not your airspace, not your information.
The second 'hurt' is one I already described. One of the most common activities I would want to engage in on my station is to test things. Shoot armor configurations/ship design sections. Build ships and shoot them to test armor types, do science info gathering, etc. Practice dogfight with real ships and real ammo. Have mock FPS fights with friends. Shoot a buddy's head off for making a bad pun, etc. Always-on godmode prevents all of this. Disabling any of that (via a setting/toggle) also disables your only form of protection. I'd feel MUCH safer by preventing undesirables from even getting close, rather than just being in godmode.
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Yeah that would largely resolve that issue, but also open up more and more opportunities for "true griefing" as in, +3 allies being able to troll people by trapping ships, trap the spawn locations of endos, preventing people from taking off, etc. Yes, you can just revoke the +3, but then you're back in reactionary, faction chores territory, especially since a very limited number of people will be able to change that kind of large-impact setting.