All the components are supposed to hit the engine assembly line nice and clean already. Adding an active flushing/cleaning station to the assembly line is probably too expensive and logistically difficult, when it shouldn't ever be necessary in the first place.
Flushing the engine later on, after it has ran for thousand of miles or the customer notices an issue, would do nothing. The damage to the main and rod bearings is already started. At that point, the thicker oil helps prevent further damage to the bearings. Once the rod or main bearings reach a critical level of damage, they can quickly seize up and stall/lock the motor.
Yes the basic engine design is old as dirt. There is nothing structurally incorrect about the crankshaft/connecting-rods/main and rod bearing design in this motor. But any engine that sends and substantial debris down into the main and rod bearings is going to struggle to live for long.