If you add too many hits before the doom extension, j.L will not combo after S. I do a different doom combo in that situation though. Here is a Dok/Dorm/Doom combo with the doom extension highlighted.
(cr.H airdash j.M)x3, S, mmhs, cr.M, flight j.H, addf, S, j.H, L blaster, addf S, backdash cr.M+dark hole, L blaster (dark hole hits), cr.M,** f+H, l bomb, missles~f+h, airdash j.S, f+H, L blaster, S (missles hit), sj.H, L bomb, addf j.S, cr M, L blaster, HBR DHC stalking flare or Chaotic Flame**
Also, one last thing about the unblockable setup is that with good timing and fast attacks some characters can mash on lights to hit MODOK before he gets into airthrow range. Inserting certain assists into the setup like I mentioned earlier will let you trade and hit confirm even if they try to mash to avoid your air throw. This is assuming you are doing the f+H, L bomb, f+H, add, cr.M, airdash airthrow setup. For my team I can use either dark hole or missles during the setup and when I move in for the air throw if they jab me out, they get caught by the assist and you can confirm with airdash j.S. With the same assist timing you can guarantee to hit opponents mashing before or after the airthrow attempt to guarantee the unblockable.