Exactly. You can't measure the individual battery voltages if they are connected in parallel.
My point was that @Hillbillytnt's comment that a parallel battery setup plus a dual voltmeter was "more useful" than a dual battery setup with an isolator made zero sense, as both meters would read the exact same voltage all the time. I don't understand how that is useful at all
Bottom line, running a dual battery setup with an isolator IS a parallel battery configuration (double capacity, same voltage) but with the added failsafe that, if discharge occurs, you'll always have at least one battery. If you drain the AUX battery, no big deal, start the machine and drive. If you lose the primary battery, you have a full AUX battery than you can jump the primary battery with in order to, again, get home.
IMHO, there is far more benefit to using an isolator than just eliminating the worry of getting stranded because you want to listening to the radio while the key is off. What if a wire gets damaged and shorts out? What if you have other accessories connected to an always-on 12v source (many do this for certain accessories) and you inadvertently leave the accessory on when you put the bike away? What if one of your two batteries sustains damage (e.g., a hard jolt results in some of the internal plates getting jammed together)? In any of these scenarios, you're losing BOTH batteries, not just one. Losing a battery can be as benign as having to be jump started to get home or as hostile and costly as having to buy TWO new batteries.
Glad you went with an isolator. It's a small price to pay for peace of mind.