1st post on the forum, big fan of the Ceriatone OTS kits, thanks for taking the time to read and respond.

This is likely a dumb question, but does the kit option 1, with an unassembled board include an updated layout?  OR is the online layout not reflecting some connections that are on the bottom side of the board, but just can't see it on the layout diagram? I was looking over the layout of the OTS Lunchbox, some of the turretboard wiring appears to be missing? Example: What is the recommended wiring of the two DPDT relays on the board?

Again, apologies if this is a known thing and I'm just late to the Ceriatone builder party.

Just because it is PCB doesn't mean it can not be modded. 
I would think the deep mod switch could be added to the tonestack.
Also I think a few people have changed resistors to flavour the OD. 
And you can change transformers. 
But not sure what else you can change or would want to change...