Rectifiers take a little bit of getting used to, but they're absolutely awesome sounding amps once you get them dialed in. I generally play on Vintage or Modern of the 2nd on a 3-channel or 3rd on a 4, gain around 2 o'clock, bass most of the way off, presence low, mids maybe 2-3 o'clock, treble around noon. It sounds like it shouldn't make any sense, until you consider that the knobs have to cover three WILDLY different "channels"with totally different responses.
If I get a chance to try out that pair again, I will try exactly that as you suggest.
Knowing only the Marshalls when it comes to big amps I put on a "heavy metal" setting on the Boogie and no matter how much distortion I got, there was almost like a ghost channel there with a very clean, midrangey clean tone in there, too. It was going through a single 4x12 cabinet but it sounded like a distorted cabinet paired with a cabinet playing the notes totally clean. It was almost stereo sounding. The Mesa heavy metal setting was a small switch that had "metal" or "heavy metal" on one side of the switch and "blues" on the other side. I don't see it on most current Dual Rectifier but on this older one, it was there.
When I fooled with the confusing Mesa Boogie panel I somehow made the traditional single coil pickup on Ibanez sound like a fat humbucker with just a hint of a strat type tone. It was really amazing, almost like it was a dual blade single coil like the hot rails, but only cleaner. I don't think it's the pickup but something with the amp. I know it's the type of deal where I would get what I want if I had hours to fool with it and certainly not as straightfoward as JCM 800 with clean and distortion footswitch and no reverb.
Close up the Boogie didn't sound good with a distortion tone and a clean tone, but I take it 20 feet away if played live that underlying clean tone on metal setting makes individual notes cut through the mix. I like Kirk Hammet's clean sounding leads and I used to attribute that to the EMG 81 cutting through like a knife but maybe it's the Dual Rectifier he uses more than even those active EMGs.
I know a Marshall can sound nice, warm and saturated on stage, and maybe get a sound that's pleasing to me right there, but often this leads to a super muddy tone in audience and it's just a bunch of loud mush. So I try to make the Marshall sound cleaner than I can stand because I know that translates into less mush out in the audience. Without soundguy, you have to kind of guess and there's nothing worse than that amateur tone many a clueless guitarist gets with too much mush, effects, and lack of clarity. I am sure I played many a gig like that at first but I always ask for honest opinions and learned early on that a good bit of clean helps with the mix as does a good midrange. It's very rare that a good tone to one's ears onstage translates to a good tone out in audience and thus the use of earbuds. And even then, some players only use form fitted to ear units and that too can make a big difference. I like the idea of playing live but having the actual sound of what it would be like in the audience piped into the ear buds.