Well, not every C compiler can compile every C program. You run into issues when you start using vendor specific additions (i.e. stuff that is not defined in the C standard). The same goes for assembly language, only there is much less standardization when it comes to assembly language. (The CPU vendor will set the instruction set and maybe a reference assembler, but beyond that everything is fair game.)
Though I'm sure that you could get away with assembling the same code on two assemblers if you stuck to the bas instruction set and maybe labels.
Assembler speed, the internal editor, and macros are likely the most important features while selecting an Apple II assembler.