Comparison and Omission: when to omit

Here are my two cents:
In brief, the second sentence you mentioned is correct while the first is not.

lets start with this example first:
Their descendants had migrated as far north as Alaska

after "as", there is a noun and it is still grammatically and logically correct. Why?
Because when we ask ourselves: what does "far" compare?
the answer is that we compare "North" to"Alaska", and both are nouns and logically represents places.

But when we return to the other example:
Their descendants had migrated as far north as the other kind of bee

Here, what does "far" compare?
option one : it is comparing "North" to "the other kind of bee". Maybe "the other kind of bee" is at a place which is so far in distance compared to the distance to the north

option two : it is comparing "Their descendants had migrated" to "the other kind of bee (had migrated)". This is a more plausible assumption and describes the intended meaning. In this case, "had" is needed to clarify the ambiguity and ensure the parallel comparison between two clauses.

A third case to mention is this one:
Their descendants had migrated as far as the other kind of bee

Again, what does "far" compare?
Option one: It is comparing "Their descendants" to "the other kind of bee". It is grammatically correct.
But, Is it comparing the location of one with the location of the other? maybe

option two: it is comparing "Their descendants had migrated" to "the other kind of bee (had migrated)"
This is more logical and near to the intended meaning.
To avoid this ambiguity, "had" is needed.