God is make-believe while a person's BMI is very real.
What Luke said was undeniably true. Becky's even said herself that she doesn't care about being as overweight as she is and isn't bothered what people say about it either.
Also being born in the wrong sex body is a very real medical condition. It's not like Luke just fancies having a male body instead of a female one. His brain is now and always has been that of a man and he just wants to correct a mistake that happened when his chromosomes determined which sex his body would develop as.
It's like saying that someone who's born with a hole in their heart shouldn't have surgery to fix it because it was "God's choice" to make them with a hole in their heart.
Your hypothetical example is a very poor one!
Luke's condition has nothing to do with a fictional guy who so very obviously didn't create the Universe or anything in it. That was down to science and the laws of nature!