It can go both ways for the Canadian teams. All 3 Canadian MLS franchises can be poor, and 1 will still get a CCL berth. On the other hand, if 2 Canadian franchises are around the top of the standings, only 1 will get a CCL berth with the other one staying home - even if that other one ends up winning the league.
So what? If you're a top team in MLS, you're always playing all the other top MLS teams in the USOC (besides the Canucks) every freaking year, no matter what. Or at least the teams good enough to beat those best teams.