Are you actually proposing that being a fully experienced & knowledgeable software engineer should be a base requirement for all academic research (in any field)?
If you, working as a software engineer, were told tomorrow by your manager that you needed to perform heart surgery, and that that now fell under your responsibilities in your current role, would your argument be the same?
The private sector's typical response to the problems in the article would be to hire qualified software engineers to assist researchers. Funding dictates this is impossible, so they make do.