Or that the self replicating systems of molecules merged into one (organic life on earth is base 4, containing two sets of two complimentary pairs - it potentially could've done it with just one of those sets),

Or that the same self replicating systems were the most (or only) stable systems that could be forged from the locally available inorganic molecules.

Or there might have been a catastrophe that killed off almost everything. In which case the organisms that survived might not have been very widespread before the catastrophe, or typical of what existed before the catastrophe.

If a large asteroid hit the Earth today it might be only a few subterranean extremophile microorganisms that survive. Asteroids were more frequent during the early history of the solar system.

This is true, but if that did happen presumably we could find some evidence for it, since it would be a relatively common occurrence during the period where earth was capable of abiogenesis. Because if it occurred at least twice, it probably happened many more times.

The counterpoint is that the fossil record is very incomplete when going that far back, seeing as tectonic subduction literally wipes the slate clean.