Absolutely the doubles have an isolation manifold. The primary set, on my right, has my primary second, dry suit and lp hose and spg. My left is dedicated to the back up reg that is on a necklace for just in case. Not quite DIR but close, webbed back plate using a 55lb lift wing which is more than enough.
The issue with pony systems is that the gas is not considered when you factor in your dive requirements. The doubles you factor in all the gas, 140cf, 160cf or 200cf depending on the fill and the dive requirement. With a SAC of just a little over .3cfm I also do well with my gas management, however as you know you calculate on the consumption of the gas hog in your group :-/
I will add one more thing about doubles or my heavy single configuration (when in wet suit). If you gotta wear the weight then why not make it advantageous. Most people with a dry suit end up wearing about the amount of weight that can make up the doubles. For me if I have to wear it its gotta work for me.
Hope this helps.