The warning on the black tank flush (to only use when drain is open) is to prevent someone from inadvertently overflowing their black tank up into the toilet causing a disgusting mess in the camper.
If you are attentive to it, there's no harm in using it with the drain closed. I do this every time we dump. My wife watches the level and tells me when it's getting close to full, then I pull the black tank drain handle. I do this a couple times and it makes for a nice, clean black tank.
2013 F-150 EcoBoost MaxTow, Roush tuned (415hp 506tq), lifted on 33s, R.A.S.
2013 Jay Flight 28BHS Elite (Equalizer 10K hitch)