Cost per seat mile doesn't account for all factors...
-RJ's also provide network feed from Podunk Falls, which cannot support narrowbodies.
-RJ's provide more frequency, which has some value to most customers but has a very high value to premium pax.
The big problem (for major airlines) with the current system is that while it allows competition and suppresses labor costs, regional managers prefer to avoid tail risk.
So if a lease term on a new airplane is 15 years, no regional wants to do a deal for new airplanes on a three-year feed contract. If they get left holding twelve years of tail risk that could BK them. Historically this has meant that majors end with longer feed contracts than they really need. This limits their flexibility in making fleet adjustments when conditions change, the usual result being they end up using RJ's in roles where they are not optimal because they have to do something with them (they can reduce their own narrowbodies or wholly-owned RJ's at will of course, ).
You are seeing some short-term feed deals nowdays, but those are on existing fleets where the regional was already stuck with some excess RJ's and had no choice.