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The following discussion is only relevant to diving with a twin-set.
Having two first stages means that you have a back up should one of the 1st stages fail. If one regulator fails you can simply “shut down” that side by turning off the pillar valve of the relevant side and switch to breathing off the other regulator. By having your dry-suit inflator coming off one side and your wing inflator off the other you also achieve redundancy (i.e. back-up) of buoyancy control.
Having a single regulator 1st stage off of a twin-set does not achieve this redundancy and in fact introduces more failure points due to the O-rings (at least 4) in the manifold. It is akin to taking the worst aspects of a single tank set-up (no back-up air supply or buoyancy) and combining it with the worst aspects of a manifold (the introduction of at least 4 more O-rings).
Diving with completely independent cylinders does mean that you have protected part of your gas supply but it also means that you need 2 High Pressure (HP) hoses and 2 contents gauges. This causes more clutter and more failure points (HP ones at that). It also means that you cannot access the gas from the tank that you have shut down. One final disadvantage of using independent doubles is that you have to keep swapping regulators in order to ensure that you are breathing down a 1/3rd of each. If you don’t do this you could be left with insufficient gas if the regulator on the side with the most gas failed.
The advantage of a manifold is that you only need one HP hose and one contents gauge as the cylinders are connected. The pillar valves operate at the level of the regulator and not the manifold. You can also breathe the gas from both cylinders even if you have to shut one of the regulator 1st stages down.
Above: Isolation manifold (note rubber knobs and DIN fittings).
A manifold may be a simple bar connecting the 2 pillar valves or it may include an isolation valve in the middle like the picture above. The value of the isolation valve is that it protects against a cylinder neck O-ring failure. Should this happen with a simple bar-type manifold you would lose the gas from both sides. With the isolation manifold you protect 1 the gas supply.
When diving with an isolation manifold you should always dive with the valve in the fully OPEN position. The reason being that if/when it comes to turn it off, you are leaving nothing to chance by deciding which way to turn it (and thereby losing valuable time). It will only turn one way, and that is closed.
It is also a bad idea to dive with the isolation valve fully CLOSED for 3 reasons:
Finally, rubber knobs fitted to your pillar valves are easier to turn and are better at withstanding any knocks. If one of your hard plastic knobs cracked you would no longer be able to shut down that valve.