Is the extra battery for cranking power or accessory power while the engine is off, or something else? How is it wired? Does the Anderson plug run straight to the battery or another connection point?
Just a guess on my part is that is used to keep from running the onboard battery down in the pits while they have the bike powered on to download data from a session, make changes to the mapping/strategies, etc.
Could I use the OE battery I pulled out as the second battery or do the chemical properties need to match (lithium with lead acid, etc)?
You can run it direct to starter. Long time ago I had bike with total loss and would run external battery to start it. I had foot switch wired in between.