G'day Matt,
you raise some valid points. Perhaps a consideration is that the larger APC units - not sure about the others I mentioned - are true sine wave and power condition as part and parcel of the overall protection - from the 1kVA SmartUPS up I believe, though you might need to go to the 1.5 kVA. My memory may not be exact on which models. Whatever, use the SmartUPS, not the BackUPS, as the former have better features - particularly in the management area.

With that said, PC's have switch mode PSU's anyway. So long as the power supplied is within the design input range you should get pretty good power out and the better quality ones have pretty good regulation too. Theoretically this should apply to any equipment that uses switch mode supplies. It all depends on quality and how over engineered the supply is. If it's running close to its limits it will fail sooner and not do its job as well.

Perhaps what is really needed is a true online UPS - these guys always run on the inverter and if there is a mains failure there is no switch over as it is already running - ya pay for these suckers but they are arguably the best way to go. Get one big enough and you can run everything on it - hope ya got big pockets for all the cash you'll need to buy one

Otherwise, if you connect the UPS and the conditioning equipment to the same power outlet then there should be no ground loop problem as they are all going back to a common ground connection that is close to the equipment. UPS on the gear that needs it and power conditioner on the other stuff. Should be fine.

--=-- My credo: If it's worth doing, it's worth overdoing - just ask my missus, she'll tell ya laugh --=--
You're only paranoid if you're wrong!