Looked like to me they weren’t using the concept of material thickness in Lightburn at all so were manually accounting for that. So the focal distance they were calculating was 17mm - material thickness. It’s possible you could leave 17mm as the focal distance and then just define material thicknesses for each material but I’m not familiar with that mode of operation.
It does. There is a Z step per pass in the Cut settings if you want to do this.
I haven’t seen much to recommend one vs the other on that. Serial I think is more “standard” or common. Not sure what would drive this decision one way or another. I’d actually suggest going to a network connection if you can if you have a reliable network. Oddly enough there are fewer things that tend to go wrong in that configuration.