Where to even begin, Part of this issue I feel is, as mentioned in the article, is that boys are taught from the young age to take care of their problems, which leads to more isolation. Another important reason I feel is the rising amount of "girls-only" opportunities that systematically make boys feel inadequate and since they are not able to participate for whatever reason (e.g. "its only for girls") they continue…
The majority of women drop out of the running for STEM jobs before they even go to college - something is persuading them at the primary school level to avoid tech related fields. It's the biggest reason that the idea of sexism in the workplace pushing women out of IT is absurd - because they never got there in the first place. They never even got to the college classes in the first place. Even high school vocational programs focusing on tech have girls wildly unrepresented.
And it's the exact same reason that organizations like Girls Who Code is extremely important. It's the same reason that an organization like Boys Who Teach/Nurse/Other female dominated profession would be a godsend for evening out the gender balance in those fields.
Should there be code/stem programs for boys? Absolutely. Is there anything wrong with programs that exists primarily for outreach to a gender that is underrepresented in that field? Absolutely not.