Minecraft Version 1.12.2
Forge: 1.12.2 - 14.23.1.2555
Issue: Attempting to create a world with JER installed opens the normal world creation menu instead of the special OTG one.

That seems really odd, have you tried that with only JER and OTG installed (and its dependencies ofc)

So what is the smallest possible mod set that causes this? Please be specific, also list dependencies and versions.

Sorry, Was sleeping. Just gave it a try, which probably should have thought to do in the first place, it does work with just JER and OTG. I also gave it another trying putting it back with my other mods and it still doesn't so I imagine that there must be some third mod that's also causing this weird interaction.

You'll have to find out which one, it really shouldn't be JER

Looks like the conflict is caused by Additional Loot Tables as well. Both JER and Additional function fine with OTG individually but if they are loaded together OTG's menu won't show up.

Smallest possible mod set.
OpenTerrainGenerator-1.12.2 - v2
OTG-Core.jar - Created by OpenTerrainGenerator
Jei_1.12.2-4.8.4.130 - Dependent for JER
JustEnoughResources-1.12.2-0.8.6.33
AdditionalLootTables-1.12.1-2.0.2.29

Also realize that AdditionalLootTables is 1.12.1 now, but until I tried using OTG I've never had a problem with it or JER in 1.12.2.

Not supporting 1.12 anymore.