I really appreciate your analysis of the likely cause of the issues, but I do believe the CMs at one point had mentioned a revisit of C&P might be considered.
I'm not sure if this is still accurate, but I do recall that it seemed rather convoluted to me when it just applied to EDH.
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Maybe there is a new version floating around that includes EDO C&P, it really should be available to Commanders within their CODEX resources.
There are two core issues with current C&P from my point of view.
1) Notoriety is not like reputation. It does not unlock system permits, missions, modules, ships etc. unavailable to non-criminals.
2) The current C&P does not effectively curtail criminal behavior in high security systems.
So bugs aside, I would like a more accessible system that achieves the 2 elements I have outlined.