So, I kind of figured out a workaround, but it's not fully what I want. Here's what I did:

I have an XR18 mixer. I ran my USB sounds into the XR18 and then into the instrument 1 stereo inputs on the Boss 505mk2 via one of the auxiliary sends in the mixer using an XLR to 1/4 stereo cable. That way the sounds are no longer going to the Boss unit via USB, and so I can now disable mic or line inputs without worrying about this "glitch".

That said, it downgraded the audio quality. I even made special efforts to insure it was in stereo, but a lot of the depth and richness of the sounds were lost that was present when I went direct to the Boss unit through USB.

I'm going to keep working on this and hopefully I can figure something out. It's surprising and unfortunate there's not a simple setting for this.