I don't see any problem at all using a 2-prong device with your conditioner and other devices that have 3-prongs. As Stan indicated there may be better results in terms of hum and noise using one orientation rather than the other.
You can assess that either by trial and error, or with a polarity direction finder as he mentioned, or, if you have a voltmeter, by measuring the ac voltage between the tuner chassis and ac neutral (the wider of the two parallel prongs on the outlets of the conditioner). Whichever orientation gives the lowest reading will ordinarily be best. That reading MUST be taken, though, with no interconnect cables connected from the tuner to any other components, just with its ac power cord connected. Otherwise the reading will be meaningless.
As you've probably read, the key to avoiding the problems you mentioned with ground potential differences between multiple dedicated lines, if you are using single-ended interconnects, is to use interconnects which are both high quality (specifically with respect to having low shield resistance), and as short as possible. Components with balanced interfaces are much less susceptible to that kind of problem.