Why doesn't analogWrite() protect its writes to 16bit registers?

I thought this was backward, but you mean that you should configure a non-8,9,10 bit WGM mode, like WGM=0, before initializing the registers so they don't get masked.

I noticed this section in the ATMega datasheet that seems to say ICRn can only be written in modes that use ICRn for TOP, not the 8,9,10 bit modes: