I'm happy to help. I used pixelmath as a quick way to try out calibrating with the dark & bias. Normally you'd just use the usual suspects to get the job done. I checked the median values with Statistics.
I don't think there is a way to add a pedestal in BatchPreProcessing but maybe its hidden somewhere in the settings. You can do it using the ImageCalibration tool by adjusting the output pedestal. I've not used it myself but it may do the trick for you.
As to the dark and bias frame median being higher than the light frame, normally I'd expect to see a light frame median that is at least a little bit higher than an uncalibrated dark, as the light frame would contain the bias signal, the dark signal, plus the background of the image. In narrowband it can be less of a difference than LRGB due to the lower amount of background light getting through.
The difference I see in your frames makes me think maybe something changed with the camera settings between capturing the bias & dark and the actual light frame exposure, or the lights were already calibrated possibly. At least it begs the question why a dark or bias frame w/ no light might be brighter than a frame that was exposed to light.