I think it is apples and oranges. For many, the difference is one sells popcorn and the other sells cookies. For my family, we didn’t like how the local Girl Scout org was run and didn’t like the program. The Girl Scouts program IS about empowerment and, to some degree, being the best Girl you can be. Cub/Boy Scouts were never about being a Boy. It was about Doing Stuff. And about Doing Good Things for Your Community and even Being Good Even When You Want to Be a Little Shit. A lot of it is hokey and feels like a 1950s civic lesson, but you get out of it what you put in, as they say.
Churches, which account for at least half of the sponsorship of Boy Scout troops, mostly despise the Girl Scouts for various reasons.
Maybe that’s a regional thing, but all of the Girl Scout troops near me are Church Sponsored.