Good point, contesting claims should only be possible if the parties are hostile towards each other. A possibly interesting edge case would be a unilateral declaration of war. However, some mechanism might be required in general to ensure consensual PvP, either as a server setting or moderation guideline, or between players themselves in some form of opt-in or -out.
A neutral or allied faction should have no negative effect on existing claims or influences, maybe even contribute to the influence of the established party (through trade and general traffic, tourism, what have you).
Please don't feel offended if much of the following may seem obvious or repetitive, and please voice concerns if you feel it doesn't make sense ; )
Generally, any individual ship would only exert influence over a limited volume of space, like the n^3 sectors that were discussed earlier, possibly depending on its mass or some other statistic. Influence in that volume would increase over time if uncontested, and once a certain threshold is crossed, the whole (16^3) system might count towards faction space. This threshold could be reached immediately if a station claims the system as it is now, or even a station might need some time to build enough influence.
Likewise a contestant would have to maintain a certain presence in order to build enough influence, and once that reaches a certain threshold, the region/system would count as contested.
If a system is claimed and controlled by a faction, it should be in their own interest, and fall in their own responsibility, to limit hostile presence there.
Of course, if neither peace nor victory is an option, both parties might settle for reduced, diminishing boni, and contest along happily ever after until the region is exhausted.
During the time the system itself is not claimed, maybe only the directly "influenced" space might count as faction space, or it might give no benefits at all until faction points are spent to make it "valuable", as an abstract development of infrastructure.
Every time period (could be the same as faction turns), in any influenced region without sufficient presence to renew the influence, a flat value is subtracted from the influence total, such that a region will return first to a claimed, and later a pristine state after continued absence. Game play considerations may or may not require this to follow a logarithmic function (higher influence=higher decay), to cap possible gains with asymptotically diminishing returns.
If a region (n^3, or entire system) is contested, the contestant's influences might be subtracted from each other, with the difference given to the highest contributor, until all but one party leaves. Being contested might result in a periodic subtraction of an additional flat value, such that if a region is contested long enough, all parties would incur a net loss of influence in that region despite their presence there (again, mirroring the destructive effects of a prolonged conflict), down to no influence at all. If and when the contestants' influences fall below a certain value, the contested status is lifted. After the conflict ends, it might even take some time before any party could begin building influence again.
I very much agree with your detailed suggestions regarding player actions that should definitely be the most instrumental part of influence gain or loss, above and beyond any mere physical presence - after all, what's the point in the server playing against itself ; )
