With a post-1900 POD, I believe a Canada with different shaped provinces is the odds on favorite with a missing Quebec as a distant second and a missing Newfoundland an equally distant third. The other options are very low percentage outcomes as they would involve Canada losing her integral territory both after 1900 and well after Confederation.
Speaking about the low odds options first, given a series of continual missteps on both sides, the Quebec question could have resulted in a that province's secession and the huge problems that would have followed. The topic has been discussed here before and, aside from the true believers, most recognize the scope of the disaster in the offing for Quebec.
As for Newfoundland, while the vote to join Canada was close, joining the US was never a real option. After WW2, let alone WW1, there's no way the US would even considered "taking" land from Britain or Canada no matter the outcome of any vote. If Newfoundland had turned down confederation with Canada, London would have simply forced another referendum while also taking certain financial steps to remind the Newfies that Britain wasn't going to be paying the bills anymore no matter how Newfoundland voted.
As for different shaped provinces, I've always wondered whether the creation of some sort of small First Nation province or provinces out of the existing provinces would be plausible. After South Africa's twisted use of the concept, the term "homelands" has many negative connotations but I'm wondering about something along roughly the same lines while also being far less cynical and/or evil.
As well as consisting of marginal lands, reservations are more often than not too small to be robust economic units. In the US, leaving aside casinos and tax free cigarette shops run by folks who suddenly "discovered" they were Native Americans, only the larger reservations, like those in the Four Corners region, even come close to providing enough economic activity for their inhabitants.
So, what if Canada created a certain number of First Nation "homelands" which were also either "full" provinces or federal territories like Nunavet is? The creation of these "super reservations", First Nation "homelands", First Nation-majority provinces, or whatever you want to call them could create different shaped provinces after 1900.