It's a tough question. My inclination is to think that focusing on the more passing transgender folks in the ads right now may be part of the better long-term approach. It's frustrating and unfair because it really does not include or represent the whole community, but if the goal is to change the world, I think that P.R. principles are more important in the short run. IMO the goal is to change public opinion. Sadly, the majority knows very little about transgender people, and most people have somewhere between neutral and strongly negative opinions of us. As wrong as it is, images showing trans women who read as male is more likely to shock them and reinforce their prejudices than to bring them around. (I only mention trans women here because from what I have seen, responses to female-reading trans men tend to be dismissive more than strongly negative.)
Changing society is hard, takes time, and there are a lot of elements to be addressed. Trying to do that all at once is just not likely to work. By using images that help people develop sympathy for our cause (and I by this I do not mean sympathy for us[/]), we can help get rid of the bathroom discrimination. It does not help with broader acceptance of trans people who do not closely fit the cis-normative expectations for appearance, but it doesn't have to. That is a different enough issue that a different approach is really needed.
We do need to be careful though, and this is a worry that I had (and is raised by the article). The selfies flying around right now do rely heavily on "do I look like I belong," which is of course the opposite of the right way to frame the question. If we end up with rules that say you have to use the bathroom you most "look like" you belong in, that's not an improvement. But I still think that these images are the right ones to help people start thinking about this. They don't contain the whole discussion, but they kick things off by showing that the proposed discriminatory rules don't actually mean quite what they sound like they might mean.