I'll take a stab at this one...
The isolator should be open. This solves a few problems:
1) In the event of a massive gas loss (cracked manifold, burst disc, neck o-ring, ect.), it will be OBVIOUS where the gas is comming from. Familiarity with your gear will tell you that it's not a regulator problem. The proper thing to do in this situation is shut the isolator and breathe the last little bit of air from the offending side.
2) In the event of a reg failing, you will know exactly where the bad 1st stage is. Whichever reg is freeflowing is the reg that is broken. On my setup, if the reg on the 7ft hose is freeflowing, i shut down the right post. If it's the backup leaking, I shut down the left. I never touch the isolator. If it is the 1st stage o-ring, it won't be a very fast leak. Shutting down the post will stop the leak, and it is possible for the o-ring to reseat itself.
3) If the left post gets shut down, you might ask how do i know how much gas do i have left? Experience plays a BIG role in this. Knowing your SAC, time and normal swimming rate helps determine what you have left for the ascent and deco. It all boils down to being familiar with yourself and your system.
4) I don't dive 3rds. Personally, I'm too conservative. I usually dive 4ths of total gas. This may cut my bottom time, but allows me to have more than "just enough" gas to get out. I rely on a good SAC for a longer bottom time.
The senario I was considering was if I were to penetrate a wreck, turn at 2/3, be most of the way out of the wreck (have about 1/2 of my gas left), and have a catastrophic gas loss. Isn't it concievable that I might lose a significant amount of gas such that I don't even have 1/3 of my gas left? Know what I mean? I have contained the gas loss but may not have enough gas left to do my deco. But if I no longer have an SPG, how do I know that? I have followed the rule of thirds but am still screwed (not totally screwed, but in a hard spot anyway). As a diver with one SPG do I do my deco and hope that I have enough gas for it? Or do I head to surface and get treatment for DCI?
At this point, your buddy should be all over you. You still have some gas left and he has the remaining gas that you need to do the ascent and deco. That's what the other 3rd in his tank is for, emergencies.
Closing the isolator does conserve half of your gas. However, the only time this should be done is when you've determined that it's not a regulator problem. Reg failures are 99% more common than a manifold failure, considering the craftmanship of the ones available from DR, Sea Elite and Halcyon. It takes a lot of force to break a manifold. If this is something your concerned about, I would work on my skills as a whole to prevent hitting the ceiling.
In the event of a reg failure, shutting the isolator limits you to half of your gas. Shutting down the offending post solves the leak problem, leaving the total gas supply available to you.
If you have already shut down a post because of a reg failure, you can still donate to your buddy and be able to exit on 2 regs.
Let me give a little senario:
Diver A has a HP seat fail on the right post, so it gets shut down and he switches to the backup reg. Now, what happens when his buddy, Diver B, hits the ceiling and has a complete gass loss?
Can they both make it out? Buddy breathing is too slow and cumbersome to exit efficiently on the remaining gas.
They can get out and do deco as if there was no reg failure. The donor gets on the working reg and the buddy gets the failed reg. I know what your thinking, why in the hell would the OOG diver get the broken reg? The reg is broken, but not useless. The OOG diver can now get behind the donor and feather the knob of the bad reg, giving him gas when he needs it.
If the isolator was shut in this situation and only half the gas was conserved, there would not be enough gas for both divers to make it out, even on 3rds.
Just my 2 cents. I hope this answers a few of your questions.