Yep. That Rat and Marshall sounded sick.
Master of Puppets and AJFA used a Mark IIC+ slaved to a Marshall amp. He boosts the lows, but the power amp is EL34 and doesn't give the bottom like a Recto type of amp does. They also used parametric EQ to shape the sound on the console. He does some things where he boosts and cuts frequencies at different places, including the custom EQ he has covered in his rack nowadays that is Top Secret.
When he uses a Triple Rec, he sets the Presence kind of high and doesn't scoop as much. I don't know what mode he uses, but I would suspect it's Modern by his settings. I'd also suspect he's using silicon diode and Bold. He likes tight and those are the tightest settings for this amp line.
From memory, his settings are something like:
Presence 1:00
Gain 1:30
Bass: 2:00
Mid: 11:00
Treble: 2:00
There's a picture floating around that could be found through Google. I've used that setting and it is very good for Metallica rhythm, even on my amp, which isn't the exact same as his. Vintage is too bassy like this.
Kirk uses moderate, user manual suggested, settings for Gain and Presence. His bass is dialed back to 11:00. Mid is around 12:30 to 1:00. Treble a little more than 1:00. I think he uses Vintage, but he runs it into a 2:90 power amp, since it's a rack preamp. His midrange and bass setting leave a lot of room for his sound to be distinct from James and work really well with Vintage mode. I'd say the back panel settings would need to be set like James to keep the tight sound on an amp head.
Premier Guitar did a rig rundown. I think an approximation could be made for EL84 power tubes, though I'm not the best person to ask about what the changes would be.