I created a Mystcraft age with the following pages:
-Caves
-Normal lighting
-Normal weather
-Stone block
-Water block
-Native biome distribution
-Standard world

This created an age with terrain very similar to the vanilla overworld. It also has caves.

Here's a screenshot of the caves in the Mystcraft age, taken in spectator mode:

Here is a screenshot of the overworld:

I'm guessing this has more to do with how mystcraft does its cave gen than a compat bug. I'll keep an eye on the mystcraft issue page.

It sounds like Mystcraft's cave generation code just copies the vanilla code for cave generation. As a result, it's not using the custom cave generator. It should be possible to create a Mystcraft page using the API that adds a "Worley's Caves" symbol. When included in an age, it would generate the custom caves.

It should be possible, but either the API is broken or I'm just not understanding how it should be implemented. But with no information/examples of other mods adding symbols though the API, I wouldn't expect this any time soon.

I recommend joining the Mystcraft Discord channel. The devs hang out there all the time.

Link: https://discord.gg/pRGH45W