I really dislike modified victories in non-objective miniature games. If there was truly an objective besides 'destroy all of your opponents ships' then I could understand having different levels of 'winning', but as it stands - it seems to hinder progress more than actually separating players based on skill. There are some modified games that are between very good opponents - rather than rewarding a well played, close game, a modified win punishes both players for the good careful play.
The real culprit (as some have pointed out) is using opponent's points as first Strength of Schedule. I would rather see Opponents Game Win % be used as a first tie breaker, especially since getting a modified loss to someone should not be worse for you than a full loss to someone (should it be better? that I'm not 100% sure).
As an alternative way to think about it (with in the current system); this should hold true for large, appropriately rounded tournaments with n rounds where 2^n > #players. If you get a 'modified loss' it shouldn't matter - your opponent is likely below you if you both end up with the same match wins.
Personally, I've only been involved in a modified result (that I can remember) 1 round out of ~40 organized games. I got a modified loss with 3 healthy TIE fighters chasing a 1 hull remaining loaded named Firespray. One more round and the Firespray would very likely have been destroyed, regardless of what he destroyed of mine. That is when the frustration about modified victories comes in - my tie breakers are now shot, the game was clearly in my favor, and he snaked out a partial win screwing both of us over in the end where I didn't make the cut based on tie breakers and he ended up on the low end with points due to his modified win. Maybe it's selection bias, but many modified wins that I see have someone who is clearly ahead with a healthy small-point ship or 2 (or 3) versus 1 large-point ship that is a sneeze away from being destroyed. (I don't seem swarm v swarm that often any more... but that's another culprit because of the sheer number of ships and timing)
As an alternative, and maybe this is just as flimsy: count hit points to determine a modified win. If one player has twice as many total hit points (hull - damage + shields) remaining as his opponent when time is called - full win, otherwise if there's no clear winner - then it's a modified based on HP remaining. Points on the board aren't as a reflective of game state IMO.