Thanks man! This is a good explanation and i wish i got something like this 3 months ago when i first contacted Apple about this. They wanted to change my speakers, go figure... As i wrote before this is the exact same square waveform that can be heard when the buffer size inside an audio app is insufficient.
Too bad that FCPX doesn't have an option to set a different buffer size and i guess this is the reason why popping doesn't occur inside Logic Pro X, right? I guess Logic uses a bigger buffer size by default so that it can handle large audio samples.
I don't know anything about FCPX, but I'm assuming that since it's a video editing app, it just uses the high level system audio API, which will not allow the software to take exclusive control of the audio interface, much less even be aware of it. Just like your web browser, it probably doesn't care.
Logic Pro X, Cubase, ProTools, and other audio-specific software actually skips CoreAudio and goes straight to the driver at a very low level. They act as their own audio engines, essentially. They can have direct control of the ring buffer (among other things) that is processed by the driver, including the allocation of the buffer, which is how these apps let you select how many "samples" large the buffer is. They are also directly responsible for writing data to that buffer, rather than asking the operating system's audio engine (Core Audio) to do it on its behalf. With that fine, low level control, these apps are basically "always on" and your system is constantly running the audio pipeline, rather than turning on an off when sounds are being played, stopped, etc.
Without actually having access to Apple's code (and I'm really not an expert), my guess is that Core Audio has some power consumption optimizations that will start and stop the ring buffer processing, but there's some type of timing or IO issue at the driver level when the pipeline starts and stops. Wild guess here; I have no evidence to back this up.
So now to answer you directly about Logic...
My guess, without looking at code and instrumenting/debugging the system, is that Logic Pro doesn't pop not because of the buffer size, but because it is "always on." In fact, most software like that end up using hacks and micro-optimizations to use an even *smaller* ring buffer to lower the latency even more!
"Samples" is a loaded term that means two things:
1. To a musician, it's a sound clip, like an instrument or something. A whole sound.
2. To a digital signal engineer, it's a momentary, digital approximation of an analog signal.
So when marketing material says something can handle large samples, they're talking about definition number one. What you want your software to do is to actually have the smallest sample buffer your hardware/software can physically handle without race hazards (which causes pops).
This was fun. I basically never get to talk about this stuff in normal, plain English. Woohoo!