I feel like the are needed as the belhousing bolt holes are slightly large as it uses the dowels to provide proper alignment.They are what does the actual alignment, and you will eevntually break bellhousings, flywheels, are wipe out front trans bushings and seals.
I bought a 2.3 mustang driver once that was missing the dowels and it constantly wiped out flywheels until I figued out the were missing.