I have heard from my rabbi that that the source R' Henkin cites is in fact a source for women to not wear pants. I also don't think the source from Pesachim 3a contradicts his teshuva on the matter, about baggy pants, because baggy pants would not expose the pisuk raglayim.
I have not seen the Meiri, whom R' Henken cites. However, Rabbeinu Chananel seems to agree with R' Henken. In his last piece on 3a in Pesachim, seen above, he clearly says "...it did not mention riding, that the act of riding is done with spreading of the legs, which is an improper way by a woman..."
In Rashi, however, also towards the bottom, 7th to last piece, the texts reads as follows:"... Because its is not fitting to mention riding AND separation of the legs by a woman..."
I'm no scholar, but notice the difference. R' Chananel identifies the act of riding specifically as a "Pissuk Raglayim". Rashi lists pissuk raglayim alongside riding, which would suggest that they are two different things which are both an issue.
In conclusion there seem to be two sides to interpreting this source. Regardless, baggy pants wouldn't be an issue. Those would really come down to Jewish societal norms and customs, I think.
The mishna in Kesubos 72a mentions consequences for a woman transgressing on "Das Yehudis". Rashi explains this to be "customs of Jewish women, even though they aren't written". The exact application of this term would be very hard to nail down in this day and age, but I think in many Jewish communities the das yehudis is to wear skirts most of the time.