Actually, when you think about it for a few minutes, to me at least it seems obvious that this is the simple understanding. Otherwise, what kind of bracha are women making? "Uh, yeah, God, you made me inferior, and it's pretty awful, but that's what you wanted, so thanks!"
Even if Judaism was misogynistic, that's a petty strange bracha. In this context, it makes sense - men are thanking hashem for giving them more opportunities to perfect themselves and grow, women are thanking hashem for making them closer to the ideal.
Furthermore, the concept that women are created closer to perfection matches many other concepts in judaism.