I knew it was near Medina(Belthasar told me that), and since the Mystics don't like Porre at that time, I first thought maybe they were using Melchior's Hut, than that big rock thingy, and last Forest Ruins. I didn't find it, so I used this Forum to find out it was indeed there.
I didn't think to go to 600 A.D., because I thought this "I wish I thought like Toma" was just this guy stating his lack of explorer skill and wish to be like Toma or something...I expected Toma to be somehow in that Lab, because he vanished. Maybe that's just me and other people might get it.
Also, in the last Dungeon: During the part with the split teams, I always have Crono in both teams, like Crono leading team Nr. 1, and after I switch, he leads team Nr. 2(yet he is still there as a NPC, meaning the one you control and one showing him at the other team).
Also, the bridge that's supposed to have both teams go on in the same Area(in order to press these 2 switches next to each other) automatically disappears as soon as a Team leaves the switch, thus the party can't be on the same "side", and the switches to go on can't be pressed.
During the Flamedungeons, I only had to play the 3 of the characters I used, but that's most likely intentional.