I think we can separate this into two distinct things:
1) Encouraging girls to participate.
2) Creating exclusive girls-only clubs for them to participate in.
And I get the sense that your issue is solely for the second thing.
My personal take is that I believe exclusive clubs exist for the same reason single-gendered schools exist. There's a school of thought out there that boys tend to be quite dominating, and this suppresses the ability of girls to get the most out of them in coed activities.
As an example, DD's STEM lab group included a boy and one other girl. DD treated me to daily anecdotes of the boy trying to take over everything, and doing it all wrong. Supported by the other girl who saw eye-to-eye with DD, she repeatedly had to shout him down, and then the girls had to waste time and materials fixing everything he'd done. Their group returned the top results.
Whether a girls-only activity is necessary probably varies based on the personality of the girls, but it would certainly seem to be necessary in many cases - see madeinuk's post on girl confidence.
I don't have a problem with 1) and actually don't often have a problem with 2) either. I think overly "dominating" boys may be worse in middle than in high school. Stereotypes exist for a reason, but interestingly my kids probably had more experiences with overly "dominating" girls than boys during the elementary and middle school years. DD is quiet and soft-spoken and has often been a magnet for overly "dominating" girls but by late middle school found effective ways to insulate (with lots of friends) herself most of the time.
Actually, my greater issue (at least recently) is the sometimes overwhelming "encouragement" of STEM for everyone. I get that we need STEM workers to maintain competitiveness and that STEM careers have great financial potential but we also need humanities people - artists, musicians, and writers.
