Yo!
Hum, that is strange, I think you are the first one that I am aware that has encountered this problem. :/
The bonus dungeon (Abyss of Tritram) is only accessible after the last war battle (Fortress of Ramchalle). Then, you will need to use Venia to teleport to the cave. The cave should start blinking in the teleport menu.
I double-checked the logic this morning and it is based on the exact same "switch" that is turned ON after the Fortress of Ramchalle's victory scene. Agram should be locked in your party at this point too.
Note: The "extended" Venia's Teleport Menu also activate once you cross the border with Chibiki near the end of the game.