The gemara draws a distinction between the case of teruma where כלך אצל יפות implies that the owner consents to what the messenger did, and the story of mari bar isak where כלך אצל יפות was not an acceptable method of determining consent for mar zutra. The distinction is that by teruma which is a mitzvah we assume he meant what he said, but when it comes to serving the rabbonim who came to visit, we are concerned that the owner only pretended to consent out of embarrassment, but in truth did not consent. The question is that serving the rabbonim should also be considered a mitzvah of hachnosas orchim and honoring talmidei chachamim. Why isn't it considered a mitzvah like teruma where we assume the owner truly consents?
It seems that the distinction is not whether it is or isn't a mitzvah, rather the distinction is whether we have reason to believe that the owner is interested in the mitzvah and therefore consents. By teruma we are speaking in a case where he appointed the messenger to separate teruma for him. Clearly the owner is interested in performing the mitzvah of separating teruma, therefore when he gives some indication to consenting to the higher quality, we assume that he truly means it. However, in the situation where the rabbonim visited, although there is a mitvah to serve them, we have no reason to believe that mari bar isak was at all interested in doing this particular mitzvah, therefore we assume that his statement of כלך אצל יפות was said out of embarrassment and does not indicate true consent.