Could I just fill the filter then and 3.1q?
Filling the filter in advance is recommended, anyway. Otherwise, your engine has to pump a bunch of oil before anything starts getting lubricated on the first startup.
I just installed my SPOOFAK, and filled the filter, put in the rest of the 3+ quarts (using oil in a gallon container, so was guessing at amounts), cranked the bike a bit with the choke off (so it wouldn't start, but would start moving oil) then fired the bike up. Let it run for about 15 seconds and then shut it down to check the level. Added what I needed to bring the level where I wanted it and was done.