Also, excuse me but "things they would like done different"? All OP asks for is not to have something he posted replaced with something else, and that's how it normally works already, it's not an "idea", it's a status quo, and it's desirable.
The slot you fill when you submit a new story to HN is community property. If you're worried about the outlandishly weird case of having your name attached to something that a mod decided was better than your submission when it actually wasn't, submit with a throwaway account.
None of this is news. The site has always worked this way. What's galling is the reason people are bickering about it now: because the moderator is making an effort to be more transparent about it.
Secondly I would disagree that the "best solution" is to email them as a single entity. Emailing the powers that be could only be the best course of action (about topics such as this) if somebody organised a mass email campaign. Seeing as the site is a medium for news and communication, I feel having this thread in full view of all eyes may not be the "best" but it is still a good solution.
Secondly, regarding your concern - I'm not a mod, but I'll take a stab at why the guidelines are the way they are:
HN, above all else, wants to be a place where hackers find interesting stories and discussions. Meta threads are generally not "interesting", not in the way that HN wants.
But that's not the only problem - the problem with "meta" threads like this are that they are very superficially interesting - after all, they concern one of the few things all of HN has in common - HN. But almost everyone here has ideas of how to improve HN - almost everyone here sometimes has things they would like done different. If every user wrote a post on this, that's all we'd talk about. Moreover, since most users are talking from a position of ignorance compared to the mods, oftentimes what they talk about will simply be wrong without them knowing it.
Therefore, the best solution is exactly what HN asks - email questions directly to them. I've never done so, but from what I understand, they usually answer.
Also, in terms of timing, you couldn't pick a worse time to complain about the moderation - this is literally the time in history that HN has been the most open and straightforward about moderation policies, and they're doing IMO a fantastic job too.