Admittedly, this needs further testing, but I couldn't find any dungeon gates in a customcubic world. I'll try testing with non vanilla, non cubic chunks worlds next.

Are you sure they don't? Try increasing the frequency in the config. In any case, the generator we're using works for all world types (it was tested with Biomes O' Plenty), so that would be a CubicChunks bug.

Huh, I guess I'll open an issue there then, after some more testing of course. Maybe I'm just unlucky.

Gateways are very rare though, by default it's 1/10000 chunks. You can make them spawn more often by changing the mod options.

I'll try that

Definitely a cubic chunks issue, set the gen chance to 1, nothing.

According to Barteks, other mods stuff wont generate in customcubic on purpose. Apparently its not reliable enough yet. Mystery solved.