Okay, so I think this might be working (sort of) as expected.
So, first things first, the side chain drastically reduces performance for a noisy setup, at least mine. So first thing to do is get rid of that.
Second thing, I was getting a lot of hum, so I had to turn the threshold knob up to be quite aggressive. Turns out there's an EMI vortex or something on my floor where I had the pedal sitting.
So how I have it set up right now, I have my splitter which goes to my 2 boosts in parallel, a TC Pre and a TS clone I had from years ago, think Deadweald Duality. They run to the same output jack, then goes to my preamp (VHT GP3), then the preamp out runs to the Muzzle, then out to my power amp.
Things I notice when using the key input: unless I turned it up a fair amount, say maybe 30% of the threshold knobs adjustment, it just was not gating. I could hear the hum be reduced that I was getting through my cab, but the LED was not changing color. This was okay, it's better than nothing, but didn't really get me the chuggy staccato like palm muting chugs. If I turned it up a lot more, it was great for that... but nothing else. I attempted to just adjust it to where the red light came on while not playing with the guitar's volume turned up, but it still wasn't performing good at all. All dynamics were gone. I know I've probably said "pinch harmonic" like 20 times in this thread, but it's just kind of a litmus test for me. If I hit one, it would ring out for maybe a second then die.
Removing the key input from it, and turning it up maybe half way so it's gating based on my preamp output now, I can set it with the guitar's strings muted so it's just barely gating, and it doesn't kill dynamics.
Maybe I'm just not a fan of one knob noise gates, I'm not sure as I've never used one before this. Performance is acceptable now, but it seems odd to me that the "key" feature (pun quite intended) reduces performance for me. This is the selling point in what has become the gold standard for noise gates. Like I don't think there's any errors on the board that I've made, it's technically working, it's just not what I was expecting. I have a friend that also got a Muzzle and it's working well for him but I'm guessing my setup is quite a bit noisier. He's going to come over when he gets a chance so we can compare, maybe I'll see if he'll let me bang a key input on his for testing (he has it jumpered at the moment) and see if it's the same deal.