I will refresh this thread with a thought model of what can happen, to prepare and pre discuss. Even though it may change, we can build a case around "what simply has to work"
The org-mind model:
Each org will gain "experience"/"influence" by each members action. The leader may be able to introduce a rule set, helping out with automatism.
--> This translates into a set of rules, branding a member as a criminal after he/she reached a certain status and thus blocking entry into parts of the org(systems)
--> The other side: if a player does lawful stuff and becomes "too good", he might be auto rejected at certain places and cannot interact with the pirate org
This way, each player's repupation has it's own consequences and reflects upon the org in such a way, that there is interactivity between org and player based on reputation.
= If Test has 150 000 000 members and builds up different branches with some pirates and smugglers inbetween, the overall rep will be influenced by each member.
= If Montoya sets the org to lawful neutral, he may get a warning when the overall rep gets too high or low and may be able to set stronger rules, which auto block certain actions.
With this model, there could be a reasonable flexibility inside each org. If rule sets would be left out, each members action can and will change the overall rep without Montoya being able to quickly react. That is why i think, automated tools need to be a thing.
-----
The case of being polarised / too good or too bad:
Player P (irate) wants to be in Test. He/she wants to be a badass pirate with very low moral. If Test as an org will have a flexible rep setting, this may very well result in Player P not being able to conduct certain missions or be granted certain missions, based on his/her affilitaion with the org.
So what will happen then?
@Black Sunder said, that we could have different alt orgs, to circumvent these sort of scenarios. This would however mean, that Player P has to leave Test main org and join Test alt Pirates. They then should have their own sub forum, which is invite only and have to struggle with the big problem: "Are we allowed to screw our main org members?" Cause at some point, this will happen.
-----
Experience will be gained, models will be presented and adjusted, players may change behaviour defined by what is considered "fun" which in itself can easily shift, depending on game system balance and so on.
I am very curious to see, how Test will evolve.