Okay, now I want CG to add Sister to the clones

If you have to say BUT after stating you're not against a trans character, then your statement isn't entirely true. Regardless why the Kaminoans didn't deem her defective is irrelevant and pure speculation. The fact that she's canon, she exists and what has been established about her is what matters at this time. 

Also, if Clone 99 was kept because "he could still oversee training and be a janitor", then clearly Sister was okay as she was still able to fight and serve. I cannot see how her identity could get in the way of her fighting and following orders.

What my question boils down to is if Sister would have varied too much from the Kaminoan's idea of an ideal clone trooper, is all. And while saying "but" after a statement typically means the statement isn't entirely true, the context of what I said matters here - trans people can absolutely exist in Star Wars - but my question is if they should have realistically survived in a clone army that is required to meet various standards. Please don't misinterpret my intentions here

Again, if the Kaminoans let her exist then clearly she's not defective much like Rex, Cody, Kix or Fives. Clones are allowed to have individual identities as we've seen. This really doesn't have to be a huge issue and you just have to accept her existence.

How are any of those mentioned clones defective?

And as an aside, I’m not just going to blindly accept what’s put in front of me. If I did, then Rey would be the chosen one and Palpatine should have returned.

Based on what you've claimed yes, Rex and the other clone troopers must be "defective" because they show unique personality traits that most typical standard clone troopers do not.

"I’m not just going to blindly accept what’s put in front of me. If I did, then Rey would be the chosen one and Palpatine should have returned." 
Wow! That is completely unrelated to the topic but now makes me suspect of you that this is just because she's transgender and nothing more. Your criticism is your opinion / headcanon and is neither fact or canon. Sister exists and she's canon.

I don't know why you seem to be getting aggressive. It is, in fact, related to the topic, because you said that simply because she is alive means she must not have been deemed a defect. What I'm saying is that just because the people in charge make a decision, doesn't mean I have to lap it up. Is Rey being the chosen one canon? Sure! Does it make sense? Absolutely not.

I say again, I don't have a problem with trans people in Star Wars. I'm questioning if it makes sense for the Kaminoans to have not deemed her defective. Now you've raised the point of unique personality traits, I realise it's not so different from the other clones who want unique identities and are not "just a number".

But to blindly claim I'm being transphobic, despite me explicitly stating so in previous comments, shows to me that you are not entirely paying attention to the points I have been making. I am now agreeing with you that Sister's decision to be Sister is simply another perfectly fine example of clone individuality, but it was never my intention to come across as transphobic. 

Great, then whether she gets added isn't a huge deal and hopefully once she is playable there'll be little discourse except for whether her abilities are broken or overpowered, not because she's trans.

TBH, with the power creep that's been going she'd be able to one shot GLs

Actually what if she was a Clone Trooper GL? I'm not sure which other Clone Trooper could be considered except for maybe one of the Null-class Advanced Recon Commandos or even one of Delta Squad.