This is crazy that you just posted this, because I've been experiencing what sounds like nearly the exact same thing recently.
I have a 2014 FR-S with just under 65k on it that I've had for exactly a month now. Stock tune. Purchased it used from a friend, so single and very meticulous/caring owner. Only AMSOil fluid and oil filter used,etc. Spark plugs (and maybe coil packs, too? @
Kaotic Lazagna) done roughly 5k miles ago.
I recently took off the loud axleback that was on there and put on a quiet one that's roughly the same volume as stock. So, I'm not sure if this symptom has always been happening and now I'm just noticing/hearing it or what. Only other relevant mods are a dry AEM drop in filter and Perrin silicone inlet tube.
But yeah my experience mirrors what you describe. Upon stabbing the throttle for a quick rev from the resting idle of ~600rpm, there is a brief sound that I would describe as a rattle/knock, immediately before the revs rise. Sometimes it is louder than others, but it's fairly easy to replicate.
If I feather the throttle slightly to raise the RPMs and then rev, no noise. Similarly, if I rev repeatedly without letting the revs fall back down to the resting idle, no noise. It's only when revving abruptly it from that default idle state.
Also worth mentioning, because I don't know if it's relevant, and I also can't say for sure if it was happening before this event. I had a strange experience last weekend where I took the car out for about 30 mins of freeway driving, and when I got off I was waiting at a stoplight and the idle rpm was dipping and the car felt like it wanted to stall. It did this at a few more lights and eventually it dipped so low while I was waiting at one that it stalled and I had to restart it and continue home which was only a few minutes away.
Upon getting back into my driveway, I noticed the revs dipping again down to the point where the DRL LEDs would briefly shut off before the revs climbed again. I thought it might just be the idle hunt issues that some of the early factory tunes had, but when I went to start it the next day after ensuring the battery was at 12.2v it only ran for three seconds before dieing/stalling.
I tried restarting it a few times and the only way I could get it to stay running is if I held the revs around 1,500-2000rpm for around 15-20 seconds. It sounded absolutely horrible while doing this which made me think bad gas, but turned out to be likely just a bad AFR. After doing that though, it would then idle normally on it's own. However, when I revved it during this time, it sounded like it didn't want to rev and I heard some knocking. This is when I believe I first heard the "knock upon idle rev stab" symptom.
Long story short, I ended up removing the MAF and cleaning it with MAF cleaner spray, and the problem went away. No more stalling, car now starts and idled fine. Did a test drive and it pulls hard as well, felt fine.
However, now I'm wondering about that strange noise that I hear now upon quick/abrupt revs! You mentioned that your OFT was identifying the event as a knock. What data point did you use to determine that? I'd like to be able to use the realtime data display or the logging feature to see if my OFT also identifies it as a knock event. Again, my car is currently still on the stock tune.
Anyway sorry for the long post, just excited about possibly getting a better understanding of what this is and why it's happening. On my old 2013 FR-S that I owned for 7 years I never noticed this strange noise when revving.