Using the Beta Plus worldgen setting(from the beta plus terrain generator mod) for custom dimensions causes structrues to generate regardless of MapFeatures being set to 0. This does not occur with the usual terrain generator settings.

The mod in question. https://www.curseforge.com/minecraft/mc-mods/beta-plus

Looks like that mod doesn't use the generatorOptions config or the map features disabled flag or anything else, at all. It just always generates everything unconditionally.

https://github.com/mrburger/Beta-Plus/blob/1.12.2-Backport/src/main/java/com/mrburgerUS/betaplus/beta_plus/ChunkGeneratorBeta.java

So it's not possible to do anything in JED to make it work. This would need to be changed/fixed in that mod.