IIRC most forks have "optimistic" travel specs, which include (i.e. do not account for) sag. so a 100mm fork with 20mm sag has 80mm travel. I think.
Tosh, the 100mm is the travel, i.e. how far it moves so yes your right 100mm travel is 25-40mm sag and the remainder. But thats how its done, the optimism might come in where you have a bump stop or a very progressive air spring that limits it from reachig the last bit of travel.
You might need to run the rebound slightly quicker when at full travel as the fork has further to extend and a slightly lower spring rate pushing it allong.
Set it for your optimum travel and you'll just have to accpet that tis never going to be perfect at any other point.