It doesn't sound like you're doing anything wrong at all... but you can't change her reactions, and so far what you are replying with seems to set her off. It might be a hormonal issue that will settle down, too - it doesn't seem like she's deliberately being manipulative, but her emotions aren't going to respond to logic. And in the meantime, you still need a solution.
You sympathize with her because she's trans, and you love her dearly, but all that still doesn't mean she should be able to get away with hollering at you and scaring your son. Can you try asking her at a neutral time why she seems to react that way, and what she would *like* you to say? If you don't get a helpful answer (and not everyone wants to psychoanalyze themselves for fun, so you may not), you could reply the next time she asks how she looks with something like "You know I love you, but everything I say here seems to hurt you, and I don't want to do that." Say it as gently as possible, but then walk away, if you can. If you can't win, the only thing you can do is not play.
(The "random compliments at another times" is great advice, too.)