I've been pushing for different victory conditions for a while.
My favorite is reputation gain. You'd only get the best quests (and reputation reward) from allying with a race and they'll demand that you declare war against their enemies to give you their best quests. This is really important to get you caring about what the quest system generates IMO. Betray that closely allied race and you lose reputation, which takes you further away from victory.
I don't have a vested interest anymore, but I would think that this would be called vendor lock-in. You would never be free to backstab or switch alliances without penalty. Also, grinding reputation has never been fun. Ever. Having multiple win conditions is a good thing, but I think it would be better if that condition was something the player set (or had a hand in setting). The way that Crusader Kings 2 does it is very satisfying in the sense that as a player you decide what you want to do. Your choice in starting country and year plays a big part, but as a player that makes you think, "I wonder how far I can take this?" The computer keeps score.
Right now, I don't think drox is well-defined as to what the game is supposed to be. Is it or is it not a 4x? Is it or is it not a Diablo themed adventure in space? Is it or is it not a mercenary sandbox? I don't know. Narrowing the win conditions would make that more clear, but it would also shut a lot of doors.
The reason it wouldn't be lock-in is because together with this, non-allied races would offer you high rewards for betraying your chosen race. So you can choose to betray the race you're allied with, but you'd take an initial reputation hit. Also, another thing I'd like to be in the game is that larger races would give you less profitable quests than smaller races (they don't need you as much). Sticking with a race as it takes over the galaxy would become less and less profitable for you, which encourages you to switch to help the smaller races.
In terms of reputation grind, the idea here is that it's something similar to 'make X money from quests', except more easily quantifiable than money. The reputation I'm talking about here is NOT from grinding faction, trying to get races to like you. It's from accomplishing big things. The small quests - finding planets and such - would give you minor rewards. The big quests - defeating an enemy, defending a planet from invasion, espionage - will give you a lot of reputation. Really, by making it about reputation rather than what's there now (making sure one race takes over the sector and allying with that race), you allow the player to do whatever he wants to do. I agree that you don't want to force the player to force the space race to end in any particular way. What you want is to tell the player: do what you do as a mercenary. Become famous by doing cool stuff. Choose which faction you want to support, and how you want the sector to turn out (one race destroying everything, cold peace... whatever).
The basic idea is, a. let the player play given the backdrop of the 4x. b. Make the player feel invested, especially in the plight of small races. c. Don't force the player to wait until the 4x resolves itself -- just long enough to 'establish a reputation' for the Drox, at which point the player can move on.