I think you've already isolated the problem. The problem is the Plexi doesn't get it's crunch for the preamp, power tube saturation (and speaker choice) is key to the signature "Marshall Tone."
To pair a clean amp and (non master) dirty amp, you usually want the clean amp to be twice the output of the dirty. For instance, if you use a 50-watt Plexi for dirty, then you want a ~100 watt amp for clean.
Anyway, mixing to two would be fairly unusable. Multi-channel amps usually rely mostly on preamp OD for thir dirty tones, it's the way 90-95% of multi-channel or high-gain amps are set up.
To get Fender and Marshall to work the way it needs to in one amp, you would need to have the dirty channel halve the output, either by switching to triode mode or switching off tubes. The switching gets complicated fast.
The problem with the kitchen sink amp you ask for is it does everything OK, but nothing great, you have to compromise something all-around to get decent tones from each channel. Hence the Rivera, which is probably as close as anyone will ever get and have a profitable amp.
That's why no one makes them.
Instead Dumble, Soldano, Bogner, Mesa, Egnator, etc. all had to do their own thing, all preamp based.
Overwise, use small amps, and mic them both.
Yeah, I think you could be on the right lines with triode/pentode switching. Mesa have those options for each channel on the MKV I believe.
This is why I posted the idea - the easy route, as you say, is preamp distortion for any amp which can claim to have a decent clean channel. Surely there must be another way? Biasing? Cascading power tubes? Power Scaling?
I don't think there's as much of a gap as people think between pure clean and a decent crunch. Sure, if you want your clean-dist range from Mark Knopfler to Pantera, you need the MV the big amp manufacturers use to cover a lot of ground. But we're talking about something for session guys, so they only need take one amp to any session or gig.