"Even if they roll everyone into the Masked Carnival "setting" they all cannot fight the same battles - they need to be tailored and crafted to each Limited Job. Without designing two separate, parallel, and yet equal content pipelines how does one fulfill both communities? One side or the other will be left anemic in comparison."

Why can't they fight the same enemies?
The whole idea around separating out BLU is that its overpowered and unbalanced. Being a solo job, at least as far as Masked Carnivale is concerned, the only balance that needs to be addressed is HP and damage of those enemies.
So long as Beastmaster and Puppeteer are on the same level, it should work fine.
Then you have one avenue of resources (which would likely be spent on something like Eureka anyway, not on extra raids) that caters to all three limited jobs.