I have actual experience dealing with various LGBT clinics in this area.
Yes they are slightly different. However they mostly follow the same guidelines. They pretty much collaborate and share ideas on how to make things better. I have the inside track on a few things at my clinic (mt Sinai/Beth Israel NYC) but I'm not sure I'm at liberty to disclose. Let's just say that some of these organizations are working to make everything more accessible to everyone regardless of income and also help those with insurance who might otherwise be navigating a nightmare.
As far as protocols go for hormones and treatment and informed consent they generally follow standard guidelines based on WPATH guidelines. Callen-Lorde in NYC has been a major driver of informed consent and it was developed their protocol in conjunction with major clinics such as Fenway, Howard brown and Mazzoni. So all of them pretty much follow the same protocol.
http://callen-lorde.org/transhealth/Long story short - if you go to one of these places you will be well taken care of.
As for it being too cheap to be true, they are funded by donations and they get funding as a community health center catering to an underserved community. They bill sliding scale to help out low income people and people without insurance. They are informed consent which basically means - you're an adult, you are presented with the risks, you acknowledge and sign and you get treatment. There is little, almost no gatekeeping. I do informed consent through mt Sinai Beth Israel.