In brief:
It was mentioned to me that my referencing Perceptor as part of the Ark's crew in my Holding Out For a Hero storyline,
Bonus Scene 7 is a G1 continuity error. To some extent yes this is correct since he is one of the many bots who “mysteriously” appear as part of the expanded crew. Sorta like all the generic Decepticon seekers who all of a sudden disappear.
Regarding the Autobots who all of a sudden are present in season two, the popular explanation seen in fan fic is the additional crew appeared later by insert your favorite method here. My favorite method, actually seen a fair amount in TF fan fic is they were indeed part of the original crew, just not on the bridge of the Ark. This usually places them in various other parts of the ship and it takes the original 19 some time to dig them out/gain access to those parts of the ship/revive them from transport stasis/etc. I lean towards this theory as it makes more sense to me when trying to make sense of a 25-year-old children’s cartoon whose creators didn’t worry too much about continuity in the first place; this was just one slag'n big toy commercial to them.
Further justification for my leaning towards the explanation I use is to take a look at the ships Nemesis and Ark. In the cartoon, the size suggests the ability for more crew. The Nemesis specs give her a full crew compliment of 200 Cybertronians, though she was “designed to maintain maximum combat effectiveness with a minimal crew.” (So what exactly is minimal?) If we assume the Ark to be smaller than Nemesis, but larger than a “shuttle” -and she must be larger than a shuttle since it was shown in Beast Wars season 3 that she had carried her own shuttle- we can assume she could host a fairly large crew compliment. (So what is fairly large?) I fully believe though that neither ship launched with a minimum nor maximum crew. So there, in a nut shell you have my view on crew. So that's why in the chapter mentioned above Prowl tells Jazz Perceptor is going. Besides, of all 19 season 1 Autobots, not all of them were on the bridge either.
So I'm curious now. What's you favorite explanation? Anyone?