There's only two ways for Threshold to win the scenario: either all Threshold models must leave the table from the Lurker edge, or all Lurkers must be removed from the table. Thus if any Threshold models are removed due to injury, it's impossible to achieve the first victory condition; no skill or map pieces are awarded unless you can wipe out all the Lurkers before they get you. It's extremely tough to get everyone across the board in once piece, but that's why there's such a bonus to the map piece search roll if you do make it. Definitely the most high-risk/high-reward scenario among the basic set! We should probably specify that it's all Threshold models in the game end conditions for the next printing though, to make it more clear.
In terms of house rules: that's something I know Mike always encourages. You've bought the rules, and it's your game now. Anything you and your friends agree to do, go for it! And by all means let us know how it works, as we're very much open to ideas from players.