@mcdn, some notes before I'm mostly off for the weekend:
I'm not sure whether your supply scheme really implements
full galvanic isolation of the analog section (which obviously includes the ADC etc). It should not connect to "world" other than only via the analog ins and outs, otherwise the use of a isolated DC/DC for the audio supply voltages is moot.
In other words, all supply voltages must be derived from isolated supplies, either using the +-15V module's outputs, or a separate module for 5V/3.3V domain if more power / better efficiency is required. Ideally medical rated ones.
Also any digital connection to the world like USB for the uC must be isolated.
Alternatively, assuming all control is done via I2C, then use I2C isolators, and I2S for the ADC must be isolated as well, so that the analog section and everything connected to it is isolated from the world that way.
As for the speaker level measurement, consider some significant low-pass filters to get rid of PWM switching frequencies of class-D amps which might cause trouble of demodulation or aliasing. I would see no problem with setting a low corner frequency just above 1kHz or so as we don't need absolute precision here, only relative precision between channels/DUTs.
Also, I would not make assumptions about the nature of the speaker signals, rather I'd use an analog balanced front-end (AC-coupled, incorporating the mentioned filters) creating a re-referenced single-ended output to feed the ADC.