(a) It is not clear from the Gemara what the Halachah is. Your question is correct, though, because the RAMBAM (Hilchos Temidin u'Musafim 6:3) rules like the Rabanan who say that the Ketores separates between the Hatavah of the five Neros and the Hatavah of the two Neros, which is not like Abaye (and Aba Sha'ul), who puts the Zerikas ha'Dam between the two Hatavos.

The BEIS YOSEF (OC 48) asks your question. He answers that perhaps since Abaye said over this Seder of the Ma'arachah, it seems that this is the Halachah (at least according to Abaye), and therefore the Mesaderei ha'Tefilos did not want to change from this order. Perhaps the Beis Yosef means to say that we don't accept the Rambam's ruling, but rather we hold like Abaye who said the order "according to the tradition of the Gemara" (which Rashi explains to mean " the entire Yeshivah of the Rabanan"). The Rambam himself, by the way, does not mention the Seder ha'Ma'arachah of Abaye in his Seder ha'Tefilah (printed at the end of Sefer Ahavah).

(As for why the Rambam himself did not rule like Abaye even though Abaye said his words "Aliba d'Gemara," the PERISHAH (ibid.) writes that perhaps he holds like the ARUCH that "Aliba d'Gemara" does not mean according to all of the Rabanan (as Rashi explains), but that he said it anonymously, that is, without quoting any other source.)

(b) It seems to me that perhaps even according to the Rambam we can securely say the Seder ha'Ma'arachah of Abaye. The TUR (ibid.) explains that the reason we recite the Seder ha'Ma'arachah in our Tefilos is because we are assured that "whenever we are involved in [learning] the Seder ha'Korbanos, Hash-m considers it as if we offered Korbanos before Him" (Ta'anis 26b). Accordingly, it suffices to be "involved in learning the Seder" and clarifying it, and we do not have to recite the exact Seder of each and every Avodah in order to be considered as if we offered the Korbanos.

If so, even if the Halachah is not like Abaye, reciting his Seder is certainly considered "being involved" in clarifying the Seder ha'Avodah. (Since it was Abaye who arranged all of the Avodos in their order one after the other, it is preferable to recite his words than to mention one statement from one place and another statement from someplace else, or to just read the words of the Rambam who came much later than the Abaye.)

It is worth noting the words of the MISHNAH BERURAH at the beginning of OC 48, who says that the point of reciting the Seder ha'Korbanos is to understand it and to delve into it, and not merely to say it with one's mouth, for it is not a "Tefilah" but rather it is Talmud Torah.

M. Kornfeld