I've tried a few different configurations for the config file to try and get one of my custom loot tables to get rolled.
S:"Floor 1"=LootTable:thaumcraft/chests/loot_bags:5
S:"Floor 1"=ChestGenHook:chests/loot_bags:5
S:"Floor 1"=ChestGenHook:thaumcraft:chests/loot_bags:5
S:"Floor 1"=ChestGenHook:thaumcraft/chests/loot_bags:5

I have confirmed that the table is created properly and properly placed with the following

/setblock ~ ~1 ~ minecraft:chest 0 false {LootTable:"thaumcraft:chests/loot_bags"}

This will spawn a chest with the appropriate loot.

I dunno. Maybe instead of

LootTable loottable = world.getLootTableManager().getLootTableFromLocation(new ResourceLocation(split[1]));

it should be

LootTableManager loottablemanager = new LootTableManager((File)null);
LootTable loottable = loottablemanager.getLootTableFromLocation(new ResourceLocation(split[1]));

But someone would have to test that