How could they offer females for Olos?
Radak: Females are Kosher for an Olah on a Bamah (Avodah Zarah 24b).
Yerushalmi (Megilah 1:11): Our verse teaches that for Bnei Noach 1 , also females are Kosher [for Olos].
Radak learns from another Yerushalmi that the Pelishtim offered them. Others learn the Yerushalmi differently. Refer to 6:14:3:1 and the note there, refer to Bereishis 7:2:152:1,2 and the notes there. (PF)
How could they offer Korbanos not in the Mishkan?
Radak citing Zevachim 118b: When Eli died, Mishkan Shilo was destroyed, and Bamos were permitted.
R. Eliezer disqualified any Korban bought from a Nochri. How could they offer the cows?
Radak citing Yerushalmi Avodah Zarah 2:1: Sarnei Pelishtim offered them. 1
Radak citing Avodah Zarah 24b: This was an exceptional ruling (to permit, due to the miracles).
Why did they go to the rock in Sedei Yehoshua?
Malbim: This was Hashgachah, so the Aron could rest on it.
Who offered the cows?
Radak citing Yerushalmi Avodah Zarah 2:1: Sarnei Pelishtim offered them.
Radak citing Avodah Zarah 24b: Yisraelim offered them. Malbim - Sarnei Pelishtim commanded them, and they also broke the wagon. It was theirs; others had no right to do so without their consent.