These are good points, and I don't have great answers to them.
My weak answer is that in a field that isn't well represented in peer-reviewed academic journals, we still have to sift it by some measures. I agree self-reports are close to worthless - we could find self-reports extolling the virtues of astrology and homeopathy.
My other weak answer is that Elevator-Gate and responses to the discussion of forming a Humanist+ community make it abundantly clear that the atheist/rationalist movement is widely perceived by a lot of smart women as both passively a horrible place to be and actively hostile to anyone who says so. I haven't tried exhaustive online searches but I'm not finding even 1% of the same data volumes from women saying they find atheist/rationalist space actively attractive because of these attitudes.
I like your point about non-wood, but if someone tells you you are stepping on their foot, non-stepping-on-feet probably does need to figure prominently in your short term decision tree.
(Great link, it's short, it's to the point.)
If someone is routinely stepping on feet, it would make more sense to find out why, and offer non-destructive ways of accomplishing that. For example, if they're stepping on feet to get attention, then offering the general rule of "don't step on feet" is just setting yourself up to write an unending list of articles about "... or lift people in the air", "... or play airhorns", "...or dress as a clown", etc.
(And I know, "you're not obligated to fix other people's problems", but once you've decided to go that route, you should take into account which methods are most effective, and "don't [do this specific failure mode]" isn't it.)
One of the lessons highlighted in the thread "Less Wrong NYC: Case Study of a Successful Rationalist Chapter" is Gender ratio matters.
There have recently been a number of articles addressing one social skills issue that might be affecting this, from the perspective of a geeky/sciencefiction community with similar attributes to LessWrong, and I want to link to these, not just so the people potentially causing problems get to read them, but also so everyone else knows the resource is there and has a name for the problem, which may facilitate wider discussion and make it easier for others to know when to point towards the resources those who would benefit by them.
However before I do, in the light of RedRobot's comment in the "Of Gender and Rationality" thread, I'd like to echo a sentiment from one of the articles, that people exhibiting this behaviour may be of any gender and may victimise upon any gender. And so, while it may be correlated with a particular gender, it is the behaviour that should be focused upon, and turning this thread into bashing of one gender (or defensiveness against perceived bashing) would be unhelpful.
Ok, disclaimers out of the way, here are the links:
Some of those raise deeper issues about rape culture and audience as enabler, but the TLDR summary is:
EDITED TO ADD:
Despite the way some of the links are framed as being addressed to creepers, this post is aimed at least as much at the community as a whole, intended to trigger a discussion on how the community should best go about handling such a problem once identified, with the TLDR being "set of restraints to place on someone who is burning the commons", rather that a complete description that guarantees that anyone who doesn't meet it isn't creepy. (Thank you to jsteinhardt for clearly verbalising the misinterpretation - for discussion see his reply to this post)