Lasya Before someone who experienced this scenario chips in, I would make an effort in giving my few pointers:
1) Hope you have all the proper documentation before undergoing HRT like the GD certificate etc.
2) If the Act didn't see the light of the day when you started HRT, there's nothing that can stop you and you would not be put to the process which the Act lays out.
3) You can ask the Physiologist and the Endocrinologist to give you a certificate marked to "Whomsoever It May Concern" stating that you were Mr.X when you met them and were diagnosed with GD and that you were on HRT from this time. These will help you a lot. With these as Annexures, you can apply for gender change. (I will however find out correct information within two days).
4) What you also need in addition from the Thailand authorities point of view is the certificate from Dr. Chettawut's office confirming your SRS surgery in order to avoid any trouble after you land.
I hope someone who had gone through this will see your thread and respond.
Wishing you very best in your journey and it gave me goosebumps when you said you no longer are the same person as in the passport.