TL;DR: The site relies on discussion in Meta for clarification and detail. The help section sort of points people there for clarification, but new users rarely look at the Help Section let alone go searching Meta. Even many experienced users don't spend time researching what's available in Meta. To make matters worse, much of the Meta clarification isn't even in our own SU Meta, it's in SE Meta.
There's a ton of clarification out there (although there are still some questions that aren't definitively resolved even there). However, there is a relatively small number of fundamental clarifications to common issues that account for a substantial portion of the recurring misconceptions and unfamiliarity. Summarizing those within the Help Center would go a long way to clarifying the apparent gray areas.
I'll offer some observations on the examples in the question.
Summary:
The site relies on discussion in Meta for clarification and detail. The help section sort of points people there for clarification, but new users rarely look at the Help Section let alone go searching Meta. Even many experienced users don't spend time researching what's available in Meta. Just a guess, users who get involved with community moderation, like working the review queues, are probably the majority of users who research these issues on Meta unless they are personally affected by an issue. To make matters worse, much of the Meta clarification isn't even in our own SU Meta, it's in SE Meta.
There's a ton of clarification out there (although there are still some questions that aren't definitively resolved even there). However, there is a relatively small number of fundamental clarifications to common issues that account for a substantial portion of the recurring misconceptions and unfamiliarity. Summarizing those within the Help Center would go a long way to clarifying the apparent gray area.