In a scenario where the CFL and NFL/AFL merged back in the 60s, for example, the Canadian teams in the NAFL would be benefitting from NFL-level television and merchandising royalties for nearly half a century. That'd help level the playing field. Also, more teams might somewhat lower the average pay, at least for journeymen players compared to OTL NFL levels. More teams isn't going to mean more superstar players, talent on that level isn't really a demand-sensitive commodity.
One other point to point out - the TV market in Canada is quite heavily centralized in modern times, with CTVGlobemedia, Rogers Communications and Bell Canada all owning wide slices of the Canadian TV market and them being able to move around big sums of money for TV rights. Rogers bought the rights to the NHL in Canada for 2015-2026 for $4.2 Billion in 2013, and the NAFL would probably have such a level of popularity that that sorta money could be justified for TV rights in Canada. In terms of how much that is proportionate to NFL rights in the states, its about even. There are a LOT of NFL fans in Toronto, and a huge number of them travel down the QEW to Bills games on a regular basis, and the Bills in Toronto series was a flop because it couldn't come close to the atmosphere of a normal NFL game at the Ralph in Buffalo. (That and the tickets at first were grossly overpriced and the Bills, frankly, perpetually suck in recent times.) Having all those fans constantly packing the Rogers Centre in Toronto would give that atmosphere just fine, thank you.
As for economic viability, CFL teams aren't exactly playing in small towns. Aside from the big 3 Canadian cities you mention (and leaving aside Regina), they all run in the 750,000-1.25mil range. And Regina is bigger than Green Bay, and like the Packers, the Roughriders survive by having developed a wide fan base that spans the country.
Most CFL teams do have smaller stadiums, but keep in mind that the CFL isn't seen as being the greatest of football. The CFL does proportionally better out west, but in Ontario (where NFL coverage is over-the-air a lot of the time) the NFL clearly has the edge. It's worth also pointing out that most CFL stadiums in the West are pretty big - ranging from 32,850 in Regina to 56,300 in Edmonton - and while they are not NFL size (no stadium save maybe Olympic Stadium in Montreal is, even the big Rogers Center in Toronto), having the NAFL around to share TV revenues and popularity with could easily mean those stadiums could be built bigger (BC Place was opened in 1983, the Rogers Center in 1989, both long after the POD here) or expanded or rebuilt.