Cons of using main XLR/Balanced outs for subwoofer?

Yes. You'll unbalance the signal going to your main amps.

@atmasphere Can you explain why using the unbalanced RCA out for power amp and Balanced out for each subwoofer will cause a problem?

I also have the option of just using the RCA main and RCA 1,2 outs for each the drivers and the subs.
I thought it would be marginally advantageous to use the Balanced out for the subs since the run is >10ft.

@zdw11  Unless the preamp has entirely separate circuitry driving the RCA and XLR outputs, when driving both you will have a lower impedance load on one of the XLR signal pins (pin 2 or 3) than you do on the other. The preamp may make less voltage on the pin that has the lower impedance load, but at any rate the total impedance to ground will be lower on that side even if the output voltage is unaffected.

This will in turn reduce the Common Mode Rejection Ratio (CMRR) that is available to the main amplifier, which will raise the noise floor and possibly also the distortion. 

You won't hurt anything. But I think you'll find it simply sounds better using the ISO-MAX devices- that is exactly what they are for.

FWIW we were the first anywhere to make a balanced preamp for home use. One of the problems we encountered early on was subwoofers with single-ended inputs. Because our gear supports the balanced standard a.k.a. AES48, if someone tried to connect the subs in the manner you describe a buzz and humm would result. Balanced and single-ended operations are mutually incompatible; its either one or the other and never both. So if you have a balanced output on the preamp and a single-ended input for the subs, that ISO-MAX Jensen box is the elegant solution. They only started making them in the last 20 years or so.

@atmasphere is this true even using different outputs? Main(XLR) vs zone 1(RCA) vs zone 2 (RCA).

I will not be using the Main Balanced AND Main unbalanced outputs.
Instead, using Main Balanced out and a separate zone1/2 RCA out.

Not sure if this was well described in my post.
I appreciate your help.

Is there any harm in using the main XLR output to send signal to the subwoofers, and using the 1, or 2 RCA output to send signal to the main drivers?

Go for it, McIntosh C220 has separate buffer on each output.

@zdw11 @imhififan  has it right. Nice setup!