To answer the top-level question: presumably it's for the same reason agender, questioning, genderqueer, and all the other groups are included as well... I've seen "LGBT" become something like "LGBTQIASOMEOTHERLETTERS".

Transgender individuals are... TRANSGENDER - this seems to have more to do with biology and psychology - not necessarily what gender an individual is attracted to. Theoretically (and please pardon my lack of knowledge of currently correct terminology):

Correct.

So... Maybe I understand from that perspective - that an individual who was born with male genitalia but identifies as a woman - if she were attracted to men, I guess might be classified by some as homosexual?

My guess is, this is probably why it's lumped in. But no. A "male at birth" individual who transitions in to female is a woman. If she were attracted to men, she'd be straight/heterosexual. Unless I'm severely mistaking what straight/hetero/homosexual are... She's a woman who likes men, which AFAIK is straight. A homosexual trans woman would be attracted to women.

because she physiologically is male (pre-op).

It's worth noting transitioning isn't just a surgery. Some trans women are non-op as well. There's HRT, which is hormone replacement therapy. And after that there's a few different surgeries that can be done. Post/pre-op generally refers to their bottom genitalia (vag/dick). A pre-op trans women (who's gone through HRT) will look like a woman.

Maybe it all comes down to gender identity or something.

That's essentially the whole issue of transgender, hence the name ;P.

Are we doing a disservice to transgender individuals by lumping them in with the LGB community?

It's actually the opposite. The whole point of attaching the "T" and joining up was to give awareness to transgender issues.