Let's go through the points you mentioned:
12,000 B.C.?
* Black Omen is canonical, and you can't defeat it by going to 1999 A.D.
* After completing the Black Omen, Lavos seems to arise from the ocean floor
* Chronopolis's account of Lavos in Chrono Cross doesn't mention an eruption or appearance event in its history, but notes it happened in other timelines
1999 A.D.?
* You can leave after defeating the Black Omen and turn around to face Lavos in 1999 A.D.
* Losing to Lavos after the Black Omen plays the bad 1999 A.D. ending (though this could simply mean Lavos went back underground and waited as normal)
For 12,000 B.C.; canonically you are supposed to let Zeal fall, then defeat Lavos through the Black Omen, correct?
I think the Black Omen thing was an oversight on programming (it looks like it, I know I would have missed it). The second point, yeah, you can skip it due to Lavos going back underground and then popping up in 1999, but for the first thing, I think when Black Omen was programmed, they didn't intend for you to go straight through to Lavos and go from there. The natural assumption, and I think everyone would agree with me on this, is that given the option of wiping out Lavos in 1999, 1000, 600, or 12000 BC, we'd wipe him out in 12000 BC. The others are just gameplay mechanics from programming for the Black Omen, since they all run the same way. You end up fighting Lavos, and that's at one specific point in the programming, so when you try to leave it assumes you got there via 1999. Nothing more than that.
Kinda like old programming. Label A is 12000 BC, Label B is 600, Label C is 1000, Label D is 1999. The Lavos fight is at Label E. Label D takes you straight to Label E, and everyone probably got lazy during the programming stages, meaning they just redirected Label A, B, and C's Lavos fights to Label E. Label E, if you try to leave, takes you to Label F. Oh look...the bucket. I think, because we are looking at this as if it held true for a real world and not a game, we can ignore 1999 AD as his death point, because it's just programming locations.
I personally think the Pocket Dimension is of similar construct to the Darkness Beyond Time (no linear motion, it's just there). I think in its current form it is incorrect (after all, if it ages 6 million years, it's seen as 6 million years, but then it's also seen as the age of every second before that?). I think it should still exist, but it needs a revamped description on it. Which may, or may not, depending on the use of the current PD description, mean editing those pages. Mainly, the PD and DBT have a time value, like our world, and it corresponds to it. So, if you went to the DBT and PD 6 minutes and 02 seconds after the start of that timeline (big bang being 0 for everything), then you would arrive in the DBT and PD 6 minutes and 02 seconds at that point (the Mammon Machine is probably tied to one specific moment when Lavos had a large amount of power, thus why you can "canonically" jump to the same point fighting Lavos after defeating the Black Omen).
Otherwise, 1999 is just a gameplay oversight. 12,000 B.C. is the right choice and lines up with both CT and CC.