I'm no expert but I might be able to suggest some things to try / check on. Here's an example of one of my Axe-Fx metal sounds for a KSE cover I made in Logic X:
https://soundcloud.com/instrumentalcase/ma-curse
The parts aren't perfect as I was dealing with a lot of latency in my DAW. I only recently figured out how to use my audio interface's low latency mixer.
Anyway, here's some suggestions if you're interested:
Click on the I/O button and then adjust the INSTRU IN level so that the yellow LEDS next to the display light up when you aggressively palm mute on your guitar, but don't bring the level control so high that it turns red.
Beneath those lights you should look for the LED that's labeled OUT 1 CLIP. Make sure that one isn't lighting up red when you play at any level of aggressiveness. If it does light up, go into the preset's amp block and reduce the MIXER Level control until the red light stops coming on when you play hard.
Make sure the volume and tone knobs on your guitar are on 10.
Make sure you are using a fully functioning guitar cable, that isn't losing your signal.
Make sure your guitar's pickups are not set too low or ridiculously close to the strings.
If you have active pickups, make sure you have a fresh battery in your guitar.
Use the bridge pickup when recording metal rhythm guitar parts.
Plug your guitar straight into the Axe-Fx, to avoid any pedals sucking your tone.
Go into your favorite metal presets, click on INPUT + GATE, and turn the Threshold control down if the gate is sucking your tone too much. Start at "OFF dB" and then raise the gate to eliminate static noise, but not so much that you eat away at your own signal / tone.
For your metal tone, try an amp model like the FAS 6160 with the bright switch on, paired with a 4x12 (I use a Tv Mix #1 a lot). Before the amp, set up a drive pedal (such as the TS808 mod), with the drive knob down and the tone knob at noon, to give you more articulation and tightness (a "clean boosted" rhythm sound).
When recording in Logic, make sure that the track is free of effects / EQ (I think Logic will sometimes enable some things by default when you add a track to your project).
When adding a new track in Logic, just click "new audio track," so you don't accidentally use a Logic amp model or something.
Pan the logic track hard left or hard right for recording metal rhythm guitar.
Record the guitar part once on the track panned hard right, and then record it again for the track panned hard left. Play both parts as identically as possible. This is known as "double tracking" your guitar part, and it will give you a bigger and more modern recorded guitar sound.
Always keep your guitar in tune and your strings fresh.
Try a heavy pointed pick like a Jazz III. Play with strong pick strokes and solid string muting.
When palm muting, make sure your hand makes contact with the strings very close to where the strings meet the bridge. Hover too close to the neck and your nice palm muting can turn to mush.
Use heavy gauge strings if you like to play in low tunings. A lot of KSE is in Drop C, for which you'll want heavy gauge strings (so you can have tight feeling strings even when you tune low).
Once you have your left and right channel recorded rhythm guitar tracks (which need to be separate takes, not one recording copied and pasted), use one of Logic's mastering presets to increase the volume and punch of your recording session. Additionally, try EQing the guitar tracks with Logic's guitar EQ presets, so they sit better with the bass, drums, vocals, etc.
... Hope that helps!