Well, it was also kitbashed together over time. The typical amiga OS install has a ton of stuff that was pieced together from a ton of different sources, much of which was never expected when they wrote the OS (the various internet stuff f.x.)
So I guess its a wonder that it does work as much as it does 
I like to think of "updated" amigas like cars in a demolition derby game. Banged up pretty badly with the wheels wobbling over the place, large sections of the structure worryingly absent, was put together from the wrecks of three others, and it's also on fire. Yet somehow, it still
moves.
wb 3.1 with the commercial software of the era is pretty stable. wb 3.9 is in a twlight zone where people using it want to use whatever the latest software is, but that means downloading all sorts of weird crap to add to the system. pretty soon it's wobbling all over the place and you can see daylight through the floor.