Tried disabling Botania world gen, doesn't change the crash.
crash-2017-01-02_20.07.17-server.txt

Tried to recreate the crash with just Botania and Biome Bundle on default settings but cannot. Does it happen every time a new world is created?

The only settings changed were:
WorldConfig.txt
(Changed to .txt file for Upload)
The size of the village. Larger is bigger. Normal worlds have 0 as default, superflat worlds 1.
VillageSize: 0
to
The size of the village. Larger is bigger. Normal worlds have 0 as default, superflat worlds 1.
VillageSize: 1

and

Set this to OBSIDIAN for "frozen" lava lakes in cold biomes
CooledLavaBlock: STATIONARY_LAVA
to
Set this to OBSIDIAN for "frozen" lava lakes in cold biomes
CooledLavaBlock: OBSIDIAN

Here were the Mods I was using
http://www.modlister.com/user/Little_Pip

EDIT:Yes, tried four times, same crash.

As you have so many mods installed it's impossible to figure out what could be causing the crash, the error log is not necessarily accurate.

As far as I can tell Biome Bundle and Botania together are not cause the issue.

Got it narrowed down to these , You were correct about it not being a Botania thing.

So I assume you get a different error in the log now?