I think you are right on the money with this. I also wondered if racial undertones were meant during the Weber convo last week, especially when Amelia looked so immediately ashamed when he asked her why she was so willing to believe Jo when she knows Stephanie so much better. I got the same vibe this week, even if Jo was obvlious and Stephanie may have been jumping to conclusions. I do think that the example Jo used was clunky and made things confusing. She tried to link challenging life experiences to motivation for performance (not to intelligence or actual surgical ability) so Stephanie's rant fell a little flat to me even though I know what she was going for.
In any event, I think that what this really points to is that most of these characters can be, um...let's call it challenged with reading nuiance or exhibiting basic emotional responses outside of themselves. Penny is clearly uncomfortable? Callie: "Stay here when I leave!". Amelia is blaming the world for her grief? Owen tells an awkward story that isn't exactly addressing what she said. Alex goes to comfort a clearly grieving friend of many years? Jo: "Alex is ignorning me!". On and on...