Well, off-topic has several reasons including an Other reason, which is probably the one the moderator used since the rest didn't apply for closure for your question:
The last one would do in the above snippet. Please make sure you understand that the various off-topic reasons will vary by site. The snippet is for Meta Stack Exchange.
The "threads" you are speaking off are posts that request for specific things like harder rules or changes to that rule here, etc. The post you linked though is directly from the FAQ for Stack Exchange. Until someone raises an issue about one of those rules and there's a huge agreement in favor of the OP's position (and discussion with SE employees), these rules are technically law since anything in the FAQ are official rules set by Stack Exchange. Everyone has to follow them.
Now to answer your concerns.
My question is, is it stack exchange policy that questions violating peer consensus as laid out on any meta thread, but not violating any rule enshrined in the help center are to be put on hold and/or closed as "off topic?"
As I said, your link is actually not of consensus. It's a rule established by Stack Exchange. I believe that this was a major problem in the earlier days (probably raised plenty of times by various users) and a solution was implemented by Stack Exchange to end this once and for all.
It seems to me that if questions are closed as off topic they should (1). actually be off topic and (2). the linked to portion of the help center should be able to tell you why your question is not satisfactory.
Like I also said, this is part of the FAQ and thus is an official rule. Cross-posting is not allowed. If you go to the top/start of the FAQ "thread", it states that for "official guidance", go to the Help Center. Note that it says guidance. Rules can be put in the Help Center but they will all appear in the FAQ.
"off topic" should not be a term for "we don't like it for reasons specified in the comments even if it is actually on topic."
Your question was deemed inappropriate for the site because of cross-posting. Due to this decision, your question had to be closed. No other reason fits for closure and thus other is used.
After examining your question, I realized that the reason for cross-posting was that you didn't receive any answers after 8 days (even with a bounty) and thus thought that having more people seeing the question would raise your likelihood for an appropriate answer. Quoting from the answer of the FAQ post for cross-posting D.W (the moderator that closed the question) had put in his comment:
Ask the question on the site you think is most applicable. If, like in this case, it does not get any answer, ask a moderator to migrate the question, or alternatively, delete it and re-ask it.
You should ask a moderator in Mathematics and see if it might be more suitable in Computer Science. You also might want to ask a moderator at the target site to ensure that it is in-topic with their rules.
