In my case I have discovered a system for not getting off topic replies deleted. It consists of starting by saying "I am sorry that this is an off topic reply but....". Or to write a clear off topic reply but very lenghty, which seems "quality". Although well, that seems to me that it will depend more on who is reporting and who is being reported, I don't think it will work for everyone.
I've done that "this is off-topic, but...." thing before, but normally at least part of that post will be on-topic. And I'd also suggest that some rules have (and should have) different degrees of enforcement. In the case of off-topic replies, I definitely wouldn't want mods to be so strict that a free discussion is inhibited--because a lot of members stray from a thread's main topic. I see it all the time. Compare that rule to the one about doxxing outside of the Investigations section, and you'll get my point.
As far as the other stuff goes, all I have to say is that moderators are human beings. So sometimes they have bad days, are in bad moods, sometimes aren't thinking straight, whatever. Nobody is perfect. But I don't see inconsistencies that stand out so much that I think it's a real problem. I don't think I've ever complained about mods or the job they do, because I don't really see any of them abusing their power or being blatantly unfair. They've got a crazy job to do, so they deserve a lot of slack.