“Can an acharon can ignore other acharonim?”
Anyone can ignore anything.
“If you can pasken halachah l’maaseh based on chazal and rishonim, you can get very different conclusions. The Vilna Gaon did just that, and to a great extent so did Rabbi Joseph Soloveitchik z’tz’l and Rabbi Ovadia Yosef z’tz’l.”
So, you are equating those who permitted these girls to wear tefillin with The Gr’a, Rav Yosef Dov Halevi Soleveitchik and Rav Ovadia Yosef Zicronam livracha?
For starters they would never IGNORE earlier authorities, they might rule differently DESPITE the rulings of earlier authorities. That is quite different that IGNORING them.
“Given our strong idea that earlier authorities are greater than later authorities, it takes a lot to say that the Bavli, and a significant fraction, possibly even a majority, of the important rishonim, can’t be followed.”
Shammai and his talmidim were exceedingly greater in torah knowledge than we could ever imagine, however, the halacha does not follow them, and despite their greatness one can not decide to follow their opinions simply because they were such great people.
One can not simply take up the argument that, i am a rabbi, he is a rabbi, we are from the same time period, so, why not, let me find an opinion that disagrees with him and hang my opinion on that and run with it. If one chooses to do so, despite 500 years of mesorah not to, to me it says that either these people are so exceedingly knowledgeable in their torah knowledge that they feel comfortable discarding the last 500 years of practical halachic practice, or, they simply dont care. Interestingly enough, their own Rebbe believes they overstepped their bounds by this ruling.