Joe, Baruch She-kivanta! Your question is asked by the Tzalach (the author of Noda biYehuda). This is on 45b, at the end of the long paragraph beginning "Amar Abaye Naktinan".

The Tzalach answers that the opinion on Amud A who maintains that if the 2 want to make a Zimun they may (this is the opinion of Rav); is referring to a scenario where one of them is a bor who does not know how to say the blessings himself. If so, the beraisa does not represent a challenge to Rav since the beraisa also states that if one of them does not know the berachot the "Soffer" says them for him.

The Tzalach explains at length how he reaches this answer, but I have just cited his conclusion for the moment.

Best wishes

Dovid Bloom

followup:

Here is a look in more detail at what the Tzalach writes.

1) We can learn a lot from the incident related in the Gemara on 45b (first wide line) where we are told that Yehudah bar Ameimar, Mar bar Rav Ashi and Rav Acha MiDifti ate bread together. None of these 3 sages was considered any greater than the other 2 and they thought that our Mishnah which states that 3 people who ate together are obliged to make a Zimun, only refers to a case where one of them is a great man who can lead the Zimun. In the absence of such a leader of the group they thought that a different rule applies "Chiluk Berachos Adif"; it is preferable to distribute the blessings. So they did not make a zimun but instead each one said Birkas Hamazon on his own.

2) The Halacha does not follow these 3 scholars, as the Gemara relates that Ameimar told them that they had not fulfilled the Mitzvah of Zimun. However Tzalach writes that one can say that when Ameimar said that the Halacha does not follow the rule "Chiluk Berachos Adif", this only applies when 3 people ate together; so one must make a Zimun, but if only 2 people ate together it may indeed be that it is better to "split the blessings" and this may be the reasoning of the opinion on 45a that 2 people may not make a Zimun even if they want to, because it is preferable to split up the blessings, so that everyone says his own.

3) Tzalach writes that according to this we can say that the Beraisa on 45b presents no difficulty to the opinion on 45a (this is the opinion of Rav) that if 2 people wish to make a zimun they may. This is because if we look at the words of the beraisa "Mitzvah liChalek" we notice that it is very similar to the words "Chiluk Berachos Adif". We can indeed say that, at any rate when the discussion concerns only 2 people who ate together, these two rules are identical.

4) It is clear that the rule that it is better to split up the berachos so that everyone will say them on his own, only applies to sofrim, who know how to say the blessing. If one of the 2 diners is a bor there is no point splitting up, because anyway he does not know how to say the berachos. Therefore Rav says that if 2 want to make a zimun they may do so, because Rav is referring specifically to a scenarion where on of the 2 people is a bor. In contrast the beraisa on 45b; that it is a Mitzvah to split up; refers to the scenario where they both know how to make the berachos.

Dovid Bloom