I think that the tree analogy and "the untroubled ease of programming beneath its sheltering branches" is not applicable in his case. Having been in a similar situation, my best guess is that his company's "tree" is called Java EE and in its shadow there is no trace of any academic or industrial advance from the past 10 years.
You don't understand what pigeonholing really means.
When programmers talk about pigeonholing it usually means they like Python and want to go at Python conferences where people talk about math, science and machine learning, but they are pigeonholed in Java EE and surrounded by people who only talk about POJOs and beans.
And to top it all off, Java experience is badly regarded in Python tech companies and long term pigeonholing usually cuts you off from the world you want to be in.