I read your link, and it does not prove that at all.
Unfortunately, women are underrepresented at all levels in technology, and more so at higher levels.
The results in that paper are completely compatible with that fact, and say nothing about why the site was designed. Underrepresentation a problem that needs solving, but changing the Stack Overflow (SO) incentive system is not going to help in the slightest degree.
The stated reason behind the design is to maximize correct answers to questions, which is a reasonable and gender-neutral goal. The researchers agree with that. This does not in any way make it "designed for Men". At worst, you can say that an emergent property of this design goal resulted in fewer points for women.
Unfortunately, the small number of women at senior levels means they are going to be dramatically underrepresented in best answers to questions.
But it would be counterproductive to downgrade the value of answers, because we come to Stack Overflow for the answers!
The writers strongly disagree. From the paper: "We do not agree, for example, with the value judgement that answers have more intrinsic value than questions: without the question there would be no answer."
I'm honestly shaking my head here. No, there is no shortage of questions. SO relentlessly culls questions and yet almost 30% of the questions remain unanswered and some large portion of the rest have poor answers. Go to any technical forum and you will see the same thing.
It's more work to answer a question than pose it, and it needs more experience or skill too.
Another way to see it is this.
Having a question I need answered is a problem for me. I need no further incentive to post on SO or wherever. "I need to complete this task. I am stuck. Help."
But you having the unused ability to answer my question is not a problem for you. If I am stuck, and you have the answer to my problem, and you don't even know I exist, then this is not a problem for you.
So SO needs to reward you for coming up with the answer more than me for coming up with this question, because I am getting a huge reward by getting the answer I need, allowing me to move forward in my work, whereas you have to take time away from your work to answer questions.
Yes, I feel there are issues with SO. Yes, they are too hard on duplicates. But the tiny number of people who actively moderate on SO are faced with a firehose of crap, because incompetent people generate more questions and are worse at asking questions too.
The problem with "not enough female senior engineers" cannot be fixed by biasing SO away from the answers given by senior engineers.
It's my belief that interest in these subjects needs to be nurtured in girls from an early age, and if society won’t do it, the schools must.
Eliminating gender bias in elementary school has worked well in many Nordic democracies to result in better representation later in life.
Another possibility is this: computer programming is an objectively dull and stressful occupation most of the time. I have been lucky that a lot of my career has not been dull, and I've tried to keep the stress level down,ale with only partial success, but a majority of programming jobs are either dull or stressful or surprisingly often both, most of the time, and involve sitting in one place staring intently into a screen and typing for very long hours.
Perhaps women are simply less tolerant of this bullshit, in the same way that they are less likely to be drunk drivers or murderers.
I don’t think I actually believe this, but I can’t rule it out.