An IA is not a standard OP amp. It's basically a difference amplifier where the gain is set by a SINGLE resistor. So, if you want a gain of -1, set the gain to 1 and reverse In- and In+. The IA amplifies the difference of (IN+-IN-) and outputs it, in this case relative to a REF. So, you get differential inputs and differential outputs.
In most cases REF has to be a low Z source.
if you have ground differences and your connecting to ground, there is no big deal.
When I did data aqusition, I often used current outputs which can be referenced to anything and differential or pseuodo-differential inputs.
One instrument I worked with, actually provided the strap for ref and ground which was very nice.
One "home made"system didn't work so well, because I failed to realize that you had like 6 instruments powered from one supply. The potentiometers were referenced to the instrument itself, but the analog reference was quite different. An AMP01 or AMP02 would have worked for each channel.