That's a good question, but unfortunately the PPU cycle accuracy is a real problem. The most accurate emulators (Nintendulator, Nestopia etc.) use PPU clock cycles as their base time quantum rather than CPU clock cycles. Emulators which use the CPU clock cannot emulate very specific timing situations, especially where asynchronous events happen in the "middle" of a CPU instruction execution. So the answer to your question is that it doesn't make any difference, unless you are emulating at the PPU clock resolution. It's not as big a deal if you are emulating at the CPU clock resolution, and it makes no difference at all if you are emulating at the CPU instruction level.