It requires the least amount of thought, testing, and precaution to provide a ground-potential-free system.
Without looking at the boards or knowing anything about them, you know that an isolated supply will float to whatever the PC/USB ground is. You can then safely tie the grounds together and not have two different earth-references that might be pulling their respective ground to a different reference. (Now, in all likelihood, you'd be fine to just naively hook up any two old supplies and tie the grounds together, but by using a battery, you take one variable out of the equation entirely.)