Lack of healthy respect for authority typically means more fights about who will do which task and more likely to unilaterally refuse to follow random parts of code standards. It may mean refusal to close jira tasks or open them. It may mean that analysts have much harder time to convince that one person to do what is needed, again.
Software development is typically strongly team work and requires quite a lot of coordination among people with opinions. When one person decides he does not accept authority of analyst, architect or manager, yes there are consequences for whole team.
No. However "freethinkers" can launch their own companies. It is like people say that Steve Jobs would not get hired at Apple today as if it were some great insight. It is simply company is looking for a set of skills and willing to pay money for it. SJ would rather launch a new company "Apricot' instead of working at Apple.
Besides 'freethinker' is just an euphemism and part of linkedin cliches nowadays. And the definition of free is anyway restrictive and bound to cultural and societal norms.
What does these qualities have to do with being a effective software developer?
> The degree acts to filter out people who are too independent to fit well within a hierarchy.
Wouldn't people that fall into the category of "free-thinkers" make for better engineers — or at least engineers that are more capable at creating novel solutions to hard problems?