The additions are to highlight the parts of our community that are typically underrepresented, more vulnerable, and facing higher levels of discrimination (i.e. trans people, intersex people, and queer people of color).
It also helps weed out the "LGB without the T" assholes. As a trans woman, seeing just the rainbow flag flying somewhere often makes me think "is this actually a safe place, or do they hate me more than the place next door with no flag?" Usually that isn't the case, but the doubt exists, and it sucks.