Ready Your Shovels (curseforge link) outright eliminates Create's underground worldgen. I'm not sure how. It's also only for Create. Other mods; such as Quark with its stone generation and Druidcraft with its own ores, are unaffected by this issue.
Removing Ready Your Shovels restores said features.

Thanks for the report- could you link us a paste of the game log when generating a world?
Something could be throwing exceptions.

Thanks jsburger. If you're concerned for your gameplay, a good testing technique is to test with only Create, and then one by one, pair it up with other mods. There's a faster way to do it, but it's a little complicated to explain. This way is foolproof though.

Closing this.

Update on this. I generated a new world with the v.2 release build and found that it actually does generate underground features. I do not have the original world to sample at the moment. As for the log, flipping through it revealed nothing to do with any world gen at all, mostly just missing recipes from other mods. I will continue to keep track of this and will report back if anything goes amiss. You can probably close this for now.