Whenever I power down my Eagle and then power it back up again, it reboots the EFW and sets the Luminance filter as the current filter. However, if the last filter used in SGPro was the SII filter for example, it might have a different focus point to the L filter (which in my case it is by around 200 steps). I know that the auto focus routine will solve the issue out, but an option to set the L filter as the filter at the end of sequence would also set the right focus point for the L filter also. Does that make sense? 
So something like currently avaiable set focus position, but, instead of on sequence start, at sequence end so that the next session’s non-sequence (pre-sequence) activities are in focus?
Setting the current focuser position would not work, because what if your current filter is not the filter in position 1 (Luminance in my case). I presume that the option you highlighted (which does not have a tooltip explaining what it does), just sets the focuser position to the current selected filter, if so then what if the imaging sequence ended with say the SII filter, but then the following day after the system starts with the L filter, the focuser will still have the position set for SII.
Resetting the filter to position 1 (Luminance in my case) at sequence end, would cause the focuser to move to the position for L so that it is in the right place next time the system starts up.