Read the manual but I am not sure I fully understand.
I want to use autofocus. However, in the “auto-adjust per filter” what specifies if the filter change either uses offsets OR runs the 9 step routine? If I specify my offsets in the filter list and the offsets are different for some filters, what specifies whether SGP moves to the offset position and then starts capturing again straight away OR SGP runs the 9 step routine?
Confused a bit 
I’m not a pro at this but I think this is how it works
When you choose “auto focus with filter LUM” and check it off then your focus points in your define filter list become offset points.
So when you use auto focus the program will pick up your LUM filter and focus with it and then apply the offset for the chosen filter that your trying to focus with.
What I did was waited for a really clear night and figured out my focus for each of my Astrodon filters and then add or subtracted that focus number from the LUM focus number to get my offset. I then applied that number in the focus point box in my define filter list.
I don’t think the step size had anything to do with it. I think the step size is determined by the speed of your scope or the binning that you are using and does not have anything to do with what filter you are using.
I’m sure someone will chime in and elaborate on this but I just went through this myself.
Heres a copy of the post I chimed in on and got my answers for this.
http://forum.mainsequencesoftware.com/t/sgp-auto-focus-how-does-it-work/5702