Here is the script used and the world generated:
Void = forBiomes(125)
all = forAllBiomes()
Void.create("DESERT", 20000)
Void.addToGeneration("WARM", 20000)
Void.addToGeneration("COOL", 20000)
Void.addToGeneration("ICY", 20000)
all.set("color", 16421912)
all.set("name", "Void")
all.set("enableRain", false)
all.set("temperature" 0.0)
all.set("humidity", 0.0)
all.set("height", 0.125)
all.set("heightVariation", 0.05)
all.removeAllSpawns("CREATURE")
all.removeAllSpawns("MONSTER")
all.removeAllSpawns("CAVE_CREATURE")
all.removeAllSpawns("WATER_CREATURE")
all.set("topBlock", "minecraft:obsidian")
all.set("fillerBlock", "minecraft:obsidian")
Void.removeDecoration("LAKE")
Tweaker.setStage("PRE_INIT")
Tweaker.setStage("FINISHED_LOAD")

all.set("genWeight", 30)

all.set("isSpawnBiome", false)

Void.set("isSpawnBiome", true)
Void.set("genWeight", 20000)

all.registerGenBlockRep("minecraft:water", "minecraft:air")
all.registerGenBlockRep("minecraft:stone", "minecraft:obsidian", 0)

As you can see, the world generates fine, except for the fact that there are still lakes.

You are only removing lake generation in the Void biome, not in all biomes. However, you are setting everything to obsidian. Those lakes are appearing in other biomes.

I changed the command to affect "all", but I still get lakes and lava lakes.

Hmm, not really sure on this one. Some testing reveals that the LAKE generation is being cancelled, but it appears lakes are still generating. Looking into it.

It turns out that Minecraft actually generates lakes in two separate places. Once as a decoration and once as a feature. I have now added a new command that you can use with the latest build.

You'll want to add the following to your script:

all.removeFeature("LAKE")

Removing lake generation in both places should stop their generation.

Works perfectly! Thank you!