MadBadDaddy:
I found the Trans Actual document to be concise, clear and informative.
I don't consider it over-broad, it just says "don't be an arsehole to transgender people"
I don't see how 'asking questions' would be problematic, when operating within the spirit of those guidelines.
That piece on transphobia is so wide that it amounts to stating that unless trans activism can decide what rights every single person in the society is allowed to have the situation is transphobic.
In reality rights do often clash and negotiation is required. My neighbor may want a giant tree near the border between our lots and I may want to have light in my house and in my garden. We can't both have what we want, yet we might both view our desires as rights.
In reality rights often clash and that particular piece implicitly always privileges trans rights over all other rights, going as far as stating that discussing the possibility of clashing rights is transphobic. Trying to maintain the rights of female-bodied people, in particular, is seen as transphobic.
Do a thought experiment and replace trans rights with the rights of some group you don't particularly care about, say natal women. Then read the whole thing with that change.
It won't apply in all parts but it certainly applies in several parts, including where the language women have had for centuries is now stripped away from us. I think you will spot the ways the piece is not fair by doing that.