No, that's not what I'm saying. They would have two MPs, but for the constituents, when they go to vote, their vote would count the same as the vote of someone in Edmonton, because they would both be encompassed in that western Canada region. It's the region that determines one person, one vote, not the district. When they cast their vote, it counts the same in that regional total as the votes of everyone else in that region.
The district vote is to determine the merit of those local candidates. Again, you have one person, one vote, because each person in that district has the same weight in determining which candidate they prefer, but the political perception—you may be right—may be that they are being given extra voting power, even though that wouldn't be true, technically speaking. One way around this is that you could leave the Yukon with one MP, while still encompassing the larger region and having the votes count to that regional total, without giving them a second MP.
I'm cautioning against that because I don't want politicians to start playing around with who gets two and who gets one. That affects the proportionality. If you decrease that too much, you end up ruining the effect of the system, but if there were exceptional circumstances where you deem that necessary, you could do that.