Yeah -that was the first appearance of Gonzo, or more exact, the PUPPET that would later become Gonzo. Though it was the same puppet that would be turned into Gonzo the Great six years later, it wouldn't be fair to say that that was "Gonzo" in the special...especially since he had a different name (Snarl). So in terms of Muppet continuity (which is often pretty sketchy anyway...no pun intented), unless you wish to think of "Gonzo" as an actor playing "Snarl" in that special, one can't really consider that as Gonzo proper.
...but still given that the Frackles did later continue on as Muppet Monsters, and Gonzo (especially in his earliest form) more a pretty big family resemblance, it would be pretty accurate to lump him in the category of Monster and/or Frackle anyway...at least until this was retconned in MFS.
If it helps you to reconcile the differences, you can consider that though there's a close enough resemblance to a Frackle or a Monster, there's enough of a difference as to set him a bit apart (in the same way that even though he may also somewhat resemble an anteater, he knows he isn't one). The knowledge of this fact may have over the years got him wondering about his origins/heritage (and sentient intelligent beings i believe have a natural tendency to question their heritage and existence especially if for whatever reason they grow up not knowing about it). And just because Gonzo was fortunate enough to have made contact with his alien family...who's to say that other Frackles or monsters weren't alien-evolved either?