Do I get a warning before the point of no return, so I could

Yeh.

>>389348942
I think you are safe...?

>>389348942
>sidequests
>in chrono trigger
You'll know anyway, just don't go to 1999 ad.

>>389348942
The old man in the end of time will tell you which side quests are left, you can opt to finish them or not before fighting Lavos

Unless I am mistaken if you fight Lavos using the end of time portal (not the Epoch) after defeating its first form you unlock a portal inside of it, I am not sure if you can return to finish the side quests though

Do not use Epoch to go to Lavos, use the bucket at the End of Time

>>389350152
I'm at 12000 BC, just finished the Mountain of Woe. I noticed I could go to 1999 AD at any point earlier. I'm just wondering if I'll be thrown into 1999 AD automatically after I finish everything in 12000 BC?

>>389348942
As far as I'm aware there isn't a point of no return.
I've never bothered with the epoch method though, maybe that one locks you into the Lavos battle.

IIRC you will be sent directly to Lavos if you complete the Black Omen ship. At least, that's what happened when I played it recently.
However, you are free to leave and come back after defeating the Lavos shell, which is piss easy if you did most of the side quests