1) I do not think it is consistent with the Tosfos Yom Tov and Ibn Ezra because it seems that the Malachim are considered living creatures, while the Ibn Ezra is referring only to lifeless objects. The Malachim are not inanimate objects.

2) However, we find that Rashi in Parshas Vayakhel (Shemos 35:17) writes that there are lots of things which are referred to both as masculine and feminine. See also Tosfos to Kidushin 2b (DH Kashu) who gives a few examples of this. Tosfos does suggest there that there is a reason why this happens in each case, so I would like to suggest a reason why the "Panim" of the Malachim are considered masculine.

3) This is based on the Shulchan Aruch, Orach Chaim 610:4, Hilchos Yom Kippur, where the Rema writes that there is a custom to wear white clothes on Yom Kippur since we are similar to Malachim then. The Magen Avraham (#5) writes that according to this, women do not wear white clothes because they cannot be like Malachim. The source for this is the verse in Mishlei (21:22) which refers to Shamayim as "Ir Gevarim" (with slightly different vowelization than the Masorah), a "city of men."

Hence, since Malachim are "Gevarim," the word "Panim" is used in Yechezkel in the masculine form.

4) After further thought and research, I have found the following:

Even though we often find in Chazal that "Panim" is used in a feminine form -- as you point out with "Panim Chadashos," and as we have "Panim Me'iros" and other examples -- nevertheless in Tanach the word "Panim" almost always occurs in the masculine form.

See Bereishis 40:7 -- "Peneichem Ra'im," Shemos 33:15 -- "Panecha Holchim," Shmuel I 21:7 -- "Lechem ha'Panim ha'Musarim," for example. In Yechezkel there are other examples of Panim used in the masculine form; see, for example, 3:8 -- "Panecha Chazakim."

The only example I am aware of in Tanach where "Panim" occurs as a feminine word is in Yechezkel 21:21, "Panayich Mu'ados."

I do not know the reason for this exception. Is it because "Panayich" is in the feminine so "Mu'ados" follows suit?

In additon, I do not know why "Panim" is usually used in Chazal in the feminine form, unlike its usage in Tanach. However, we do find sometimes in Chazal that the structure used is more feminine. The very first Mishnah, in Maseches Berachos, states "Me'eimasi Korin." If this was the Hebrew of the Tanach it would be "Korim" instead of "Korin," but it seems that Chazal put a "Nun" at the end, which in Tanach would be a feminine form.

4) I would also just point out that body parts are not always in the feminine form; for instance, the word "Lev."

Kol Tuv,

Dovid Bloom