No, it was exactly as far-fetched from the beginning. Both the points I made -- V'Ger being uninterested in organic life and its technology being immensely beyond the Borg's -- are just as applicable to the pre-FC Borg. Indeed, the technology point is even more applicable to the pre-FC Borg, which hadn't yet been retconned as using nanotechology and whose tech looked even cruder and clunkier than it did later on.
And the whole "different branch of the Borg" thing is basically a tacit admission that they don't really resemble each other at all and that it's an enormous reach to connect them. Honestly, I don't know why The Return even bothered to refer to V'Ger at all. I don't see what it added to the story.
You have a good point about the pre-FC Borg being clunkier. However, the pre-FC Borg interest in assimilating life forms seemed more a means to gain the technology of life forms than as an end in itself like it began to seem (to me, at least) with the post-FC Borg. Also, assimilation didn't seem to be the pre-FC Borg's main goal in the same way assimilation seemed to be the post-FC Borg's goal. As far as why The Return
referred to V'ger, it was to connect Spock to the Borg and explain how he could be "the mole/traitor".