I know the option exists if you run BoP on it's own, but I'm using it inside Realistic Terrain Generation, and the gems are conflicting with gems from other mods.

Already planned as a part of #815

Wow - instant response ! Awesome - for speed and planning :)

You might be able to use an NBT editor to change the generator settings, even if you're using the RTG world type.

The settings are:

{"landScheme":"vanilla","tempScheme":"medium_zones","rainScheme":"medium_zones","biomeSize":"medium","amplitude":1.0,"generateBopOre":true,"generateBopSoils":true,"generateBopTrees":true,"generateBopGrasses":true,"generateBopFoliage":true,"generateBopFlowers":true,"generateBopPlants":true,"generateBopWaterPlants":true,"generateBopMushrooms":true,"generateRockFormations":true,"generatePoisonIvy":true,"generateFlax":true,"generateBerryBushes":true,"generateThorns":true,"generateQuicksand":true,"generateLiquidPoison":true,"generateHotSprings":true,"generateNetherHives":true,"generateNetherPlants":true,"generateEndFeatures":true}

If you were on a server, you would be able to just add that string to generator-settings and change the values, but I'm not entirely sure how it would work with an NBT editor