Right, let's untangle this - because your instinct is correct, even if the terminology's making it sound more complicated than it is. Short answer: yes, keep them completely separate - never let Blue Blood and Shimano fluid touch, in any dilution, on any tool.
Magura MT7 (Blue Blood): This one's the easy bit. A flush is just pushing fresh Blue Blood through from the caliper syringe until clean fluid runs out the lever side, cycling back and forth to chase bubbles - that's the standard method however you're doing it. There's no viscosity conflict to worry about here at all, because Blue Blood is the only fluid Magura's system is ever meant to see.
XTR M9220 (Shimano LV): The M9220 was specifically designed around Shimano's new Low Viscosity oil - it's built with different seals to suit it, so LV is the only fluid that's validated for that brake. Critically, that's not just "vs Magura" - Shimano's own line is that do not mix SHIMANO hydraulic mineral oil with SHIMANO low viscosity oil, as failure to do so may prevent the brakes from operating and result in serious injury.
So even standard Shimano red mineral oil is off-limits in an M9220 - it has to be LV, full stop. The actual risk in your plan:
The danger isn't the two systems somehow mixing in use - they're sealed, separate hydraulic circuits with zero shared plumbing. The danger is cross-contamination via shared kit: if you push Blue Blood through with a syringe, then reuse that same syringe/funnel/hose for the LV job without a proper clean, you'll get exactly the trace contamination Shimano warns about. So:
• Use a dedicated syringe/hose set for the Magura job, and a completely separate, dry set for the Shimano job • Don't "top up" one with leftover fluid from the other, even a few drops
• If you only own one bleed kit, strip and thoroughly flush it with isopropyl alcohol and let it dry fully between jobs
You're not overthinking this, by the way - treating Blue Blood and Shimano LV as two fluids that must never meet is exactly right, not overcautious.