I boil in the kitchen, ferment in the basement, and had originally thought about a setup like you describe, filling my primaries on a waist-high rack (Metro shelving) to make the racking process easier on my back and better for the beer.
I would still be considering this if I wasn't considering a chest freezer for temperature control, which pretty much requires me to load and unload from the top, meaning it'll be on the ground and I'll always disturb some sediment. I don't want to go off-topic here, but having considered the options, the trade-off I'm making is somewhat disturbed sediment for better temperature control.
I'm finding there's a lot of these trade-offs as I build out my system. I hate answers that don't answer the question so here's mine:
I manhandle the carboy from floor to laundry table and auto-siphon (with tip) into [secondary|bottling bucket]. I use the bung from the unstoppered carboy to prop it up on one side to get all the beer. I try not to actually slosh and disturb the compacted layers of the yeast cake, but beyond that, I don't bother much. The cloudiness over the top layer is mostly viable yeast, and that's all I usually get.