Wow, this issue has been bugging me for a few months and I didn't even know there was a thread on it until now.
As ZeaLitY said, the best we can probably do is infer that Lavos was never present in the Dragonian dimension based on the factors he mentioned. If we go with this, it opens up a great discussion on the factors that would determine whether Lavos impacted the Chrono world in the first place.
Was the Dragonian dimension just the result of random chance, with Lavos' path from a distant world deflected by a bit of space dust it had a probability of encountering during a long journey?
Or, if Lavos should have a 100% chance of striking the Chrono world, could Lavos actually be the result of the Dragonian Dimension? Sort of like, how in the Terminator series, there should have been an original dimension in which John Connor defeated Skynet and nobody was sent back in time, but Skynet sent a Terminator back in time to kill him, thus creating a new John Connor + Ahnold dimension. If the Dragonians got into a war with a space faring civilization in the future, one side or the other may have created Lavos as a big, spiny Terminator.
A third theory that strikes me as having a hint of plausibility is that Azala used her telekinesis to deflect Lavos' path toward the planet in the Keystone dimensions, but decided not to do so in the Dragonian dimension. Faced with defeat, Azala may have adopted the Hitlerian attitude: "My people were defeated, so they don't even deserve to live," and subsequently she used the nuclear option. Either that, or it would be like Hitler having a nuclear bomb in his bunker and decided to use it to take out as many enemies as possible in a last, desperate show of force.