The following video was posted 6 years ago but apparently was filmed in 2011 and features quite a number of men dancing in flowy skirts. It is very hard to see how many due to the size of the dance:MiS may have some footing in dance circles, but if it's been acceptable for decades, yet still hasn't caught on in the greater sphere of fashion, we need to investigate why that is.
Also, not that I doubt you, but I'd like to see some of these YouTube videos, if it's okay with you.
https://www.youtube.com/watch?v=Xyhl89yGMFA
Another dance, same band, similar time period, has men in flowy skirts:
https://www.youtube.com/watch?v=KevQxr-saFw
You can just search 'contra dance' on YouTube and pretty much any video you watch is going to have at least one male dancer in a skirt.
I'm friends with a contra caller and she is my source for 'this has been going on since around 2000, if not longer', although there's very little written record and as it seems to be mainly a USA thing, and I'm in the UK, it's somewhat difficult for me to question a large number of older dancers / callers to see if they have any recollection.
There are films of contras from the 50's ish on youtube with typical clothing in effect, so the skirts thing seems to have started sometime between then and the early 2000's.
I have not been able to find any serious studies into it as an isolated phenomenon, though the following paper addresses clothing among contra dancers generally, mentions man in skirts, and is from 2004: https://www.jstor.org/stable/4137718