In a lengthy comment on this Talmudic passage in Ben Yehoyada, R. Joseph Hayyim of Baghdad addresses this question.
He begins with a different question: how is it possible that R. Nachman was unaware of the law that one must not talk while eating? Furthermore, how could R. Yitzchak respond? The very statement he was quoting forbids making the statement! Additionally, many great rabbis throughout the generations have not followed this law, and in fact do talk while eating.
He provides two possible reasons why it would not have been problematic in this situation. The first is that this law only applied when people while leaning. In such a situation it was indeed dangerous to speak while eating, but when eating sitting upright there is no danger. R. Nachman felt justified in talking while they were eating because they weren't leaning. R. Yitzchak responded by quoting the statement of R. Yochanan. R. Yochanan's statement was short and to the point – you can't talk while eating. He didn't say that it only applies in certain situations. While a tanna can issue a vague pronouncement without delineating the parameters, an amora is obligated to explain his statements. Thus, the fact that R. Yochanan did not specify that this law is only aplicable when leaning means that it is in fact applicable even when not leaning. The reason for this is that even though it is not dangerous in such a situation, we forbid it on account of the situations where it is dangerous. R. Yitzchak felt that teaching this to R. Nachman was sufficient reason to override the secondary decree.
The alternative explanation is that while it is dangerous to talk while eating, it is irrelevant when the speech is words of Torah since the mitzvah (of Torah study) would protect them from harm. R. Nachman therefore felt justified in engaging in a Torah conversation. R. Yitzchak however felt that even though speaking words of Torah is not dangerous it still must not be done because onlookers may not realize that it is words of Torah being spoken, and they may then think that it is okay to talk about anything while eating.
This is where we get to the relevance of the statement about Yaakov not dying. R. Yitzchak was making the argument that we have to be concerned about onlookers making a mistake. He thus cited the statement about Yaakov to buttress his argument. Since they embalmed, eulogized, and buried Yaakov even though he didn't die, we see that they were concerned about the onlookers mistakenly thinking that Yaakov was a god. If so, we too must be concerned about onlookers mistakenly thinking to is fine to talk about anything while eating, and therefore we must refrain even from talking about Torah which poses no danger.
