Tosfos in Megilah 4a DH she'Af touches upon a question similar to yours. Here is what I understood from his words (there and in Pesachim 108b DH she'Af) with regard to your question:

(a) According to Rashi in Pesachim (108b, and Rashbam), "Af Hen..." means that women brought about the miracle, and not just that the miracle saved women as well as men. There is no source that shows women brought about the miracles of Sukos (the Clouds of Glory etc.) or the miracle of the speed with which Bnei Yisrael left Mitzrayim, for which we eat Matzah. Thus, according to Rashi there is no question. (This may have been Rashi's reasoning for offering his explanation of "Af Hen...")

(b) However, the other Rishonim disagree with Rashi and explain that "Af Hen..." means that women were saved along with men, in which case your question about Matzah returns. Tosfos seems to have taken three different approaches, in different places, to how "Af Hen..." applies to a Mitzvah d'Oraisa. These approaches affect your question as well.

1. Tosfos in Megilah in the name of Rav Yosef Ish Yerushalayim explains that women indeed should be obligated in a Mitzvah d'Oraisa because of the logic of "Af Hen...". The reason the Gemara brings a Pasuk to obligate women in Matzah is because the Gezeirah Shavah from Sukah would otherwise override the logic of "Af Hen...".

According to this, the Torah indeed does use the logic of "Af Hen...".

2. In his other answer in Megilah, Tosfos writes that the Rabanan instituted to obligate women in all Mitzvos Aseh sheha'Zeman Grama, both mid'Rabanan or mid'Oraisa, due to the logic of "Af Hen..."

According to this reasoning you certainly cannot ask why we don't apply "k'Ein d'Oraisa Tikun," since by applying such a logic it would be impossible for the Rabanan to impose any Rabbinic institution. For example, we may ask how the Rabanan can obligate us in Netilas Yadayim (for Chulin) or in Eruv Chatzeros, if the Torah did not obligate us to take such measures? The obvious answer is that the Torah granted the Rabanan the right to institute Rabbinic requirements as they see necessary (to enforce the laws of the Torah). If the Rabanan deemed it proper to obligate women in Mitzvos Aseh sheha'Zeman Grama although the Torah does not, that is their prerogative. It is only after the institution, with regard to the details of the Rabbinic institution, that we apply the rule of "k'Ein d'Oraisa Tikun." The original institution is k'Ein d'Oraisa by its very nature, since it is enforcing the law of the Torah. (For example, in our case it is k'Ein the laws that apply to men when it comes to Mitzvos Aseh sheha'Zeman Grama.)

3. Tosfos in Pesachim 108b seems to take another approach. Although he himself quotes that axiom of "k'Ein d'Oraisa Tikun," he writes that the Rabanan only instituted that women must observe Mitzvos Aseh sheha'Zeman Grama in Rabbinic injunctions but not in Mitzvos d'Oraisa.

According to this reasoning you may be correct in asking why the Rabanan differentiated between a Mitzvah d'Rabanan and a Mitzvah d'Oraisa, obligating women in Mitzvos Aseh d'Rabanan although they would not be obligated had the Mitzvah been d'Oraisa.

It would seem that the answer is, the Rabanan sometimes enforced their laws more than those of Torah commandments (Divrei Sofrim Tzrichim Chizuk, Rosh Hashanah 19a). Similarly, the Rabanan at times instituted broader-ranging laws than the Torah's laws because of the Chavivus, dearness, of Divrei Sofrim (see Avodah Zarah 35a, Eruvin 21b).

According to the Avudraham's principle, I can perhaps explain this point more clearly with a parable. The Avudraham writes that the Torah exempted women from Mitzvos Aseh sheha'Zeman Grama because they have family obligations (to their husbands or fathers) and their time is not in their own hands. This means that the Torah deferred to the husbands and fathers, exempting women from Mitzvos Aseh sheha'Zeman Grama so as not to prevent them from performing their respective duties.

My parable is as follows. A chivalrous nobleman always offered his butler a generous helping from the sumptuous dishes that he was served. On the nobleman's birthday, the butler brought a gift for the nobleman; a beautifully decorated home-baked cake. When the nobleman opened it, he noticed that a piece had already been cut from it! The butler excused himself for tasting the cake, explaining, "I knew you would offer me a piece, so I already helped myself to my portion!" The butler's lack of etiquette in this case is quite evident.

Similarly, the Torah can exempt women from its Mitzvos Aseh sheha'Zeman Grama in order to be gracious, so to speak, to the men who would lose out. But when the Rabanan institute Rabbinic obligations, it would be unmannerly for them to take the same approach.

Best wishes,

M. KORNFELD