The N-1 failed for lots of reasons besides having so many engines. It's designer died before it was completed. It's primitive control systems were inadequate. It's funding was inadequate.

SpaceX has already shown that with modern control systems, you can bundle a bunch of chickens together to plow a field. Having 9 engines has already helped them complete missions where one failed. The Falcon Heavy problem isn't scaling from 9 to 27 per se, it's building a new structure to handle all the new stresses that will occur, from the launch sequence to aerodynamic.