I don't think those are good examples of flanderization. Looking at JDs example, he was always that way, but was less confident in himself to show that side. A core character growth point for him is embracing his lack of masculinity while his father figure continually lambasts him for it. As he becomes more comfortable in his new job as a doctor, it would make sense he would be more comfortable being himself.
Flanderization is when a character becomes fully defined by what was initially just a quirk or feature of the character. I don't think you can summarize JDs character as 'feminine dude' . JD continues to be complex and grow throughout the series. It's not perfectly linear growth, but it shouldn't be.
I think a big reason it shouldn't be considered flanderization is he gets serious when it's necessary, he does still struggle with his masculinity some, and he grows as a character in other ways. Hell, he ends up as a strong and responsible leader while maintaining his lack of masculine traits.
Elliots example you copied is just weirdly self-countering and kinda sexist. Elliots growth was heavily centered around self confidence and self acceptance. She started out as a shallow, rich kid, know it all who couldn't take the pressure and couldn't handle when she wasn't good at something. I don't think any of those traits ended up flanderized.
There are plenty of shows that flanderize characters to a pretty extreme level. I find it weird that you would call out scrubs of all shows for flanderization.
They throw out all nuance and have absolutely no empathy or consideration that others need to live differently than them. Or hell, need to live differently than them in order to support their own lifestyle. I swear 90% of them have never lived outside the city they were born in.