Logically, I think that this could only be set in Nebulosity through Edit -> Preferences, in the Capture Output or Processing sections - but I don't see anything obvious there.
There is an option for altering the demosaic method. The default is VNG, but I have no idea whether changing this will alter the colour balance in any significant way - I guess that the only way is to try out these variations. See manual page 104.
I tend not to use the Auto Color Balance step in Nebulosity, instead relying on Photoshop to remove any imbalance further downstream - as there is a lot more control there. I have Photoshop's Camera Raw configured to process 16-bit Tiffs in addition to Raw, so get several bites of the cherry in my workflow.
In addition, if there is extensive image manipulation taking place during the workflow, it could be argued that there is almost certain to be RGB channel imbalances introduced anyway - which are best neutralised near the end.
But I do use the Adjust Color Background menu item, to neutralise any imbalance caused by skyglow.
Cheers,
Graham