No tool is perfect. The unix philosophy is a philosophy, not a dogma. It serves well in some use cases. And in the other use case, you’re perfectly fine to put the whole domain in a single program. The hammer has been there for millennia, but once we invented screw, we had to invent the screwdriver.
The point is that Unix philosophy is mostly a retroactive justification of why things are the way they are, and not really a coherent philosophy that drove the design of those things, even though it is now often represented as such.