To answer both of these questions we can suggest that Rashi did not say that the source for following a ruba d’lessa kaman is drawn from the fact that we follow a ruba d’eissa kaman. The source for following a ruba d’lessa kaman is from either one of the earlier sources cited in the Gemara or from the fact that in certain cases there is no other option. Once we know that we can follow such a rov, at least in cases where it is absolutely necessary, we know that the Torah acknowledges such a type of rov. Once we know that this type of rov is an acceptable rov, we can derive from ruba d’eissa kaman that we can follow a ruba d’lessa kaman – even in situations in which it is not necessary. This is merely a detail in how and when to apply the rov, not a source that we may follow in general.
Thus, there is no contradiction between Rashi’s commentaries. Additionally, we have explained the reason why, although the Gemara could not derive that we follow a ruba d’lessa kaman from the fact that we follow a ruba d’eissa kaman Rashi nevertheless says that we derive this aspect from there.