As someone who's serviced an awful lot of regs over the years, I can confirm that an awful lot of first stages have been ruined or nearly ruined by allowing salt water or brackish water into the first stage. I've seen a few cases where a diver has done something stupid and allowed an the inlet fitting to be come loose on an unpressurised tank under water (OW divers with pony bottles and technical divers with stage and deco bottles). However the vast majority of cases involve brackish water from a rinse bucket.
Rinse bucket etiquette frankly sucks as sooner or later you'll see some moron rinsing their wet suit in the bucket, and that very quickly increases the salt content of the water (as well as the urine content). And rinsing a BC in a rinse bucket is nearly as bad in terms of adding salt to the bucket.
Water enters the reg in the rinse bucket through either the first stage inlet, or through the orifices in the second stage if the purge button is depressed while the reg is being rinsed. If the first stage is below the second stage that's let in the water, it will run down the hose and flood the first stage. Once it's there, salt, moisture and time will ruin the first stage.
What is the purpose of soaking a sealed diaphragm first stage?
The sealed ambient chamber only ensures that water stays out of the ambient chamber, and that's only true if the seal stays intact. If it happens to be compromised, the water that is let in will be trapped there and will corrode the bejezzus out of everything in there. Divers need to inspect their "sealed" ambient chambers now and then to ensure they are still in fact sealed and dry. Unfortunately many companies used opaque diaphragms, often to display their logo on it as well, that make noticing moisture or condensation very difficult. Scubapro has the right idea using a clear diaphragm that lives under a heavy rubber trim boot that protects the diaphragm, but can just be popped off to inspect the clear diaphragm for any signs of moisture underneath.
Even if it's doing it's job as designed, you'll still get salt other places on the regulator, such as around the DIN fitting or yoke, under any trim boots, in the small gaps between various reg parts and between the port plugs and reg body on the unprotected side of the o-ring. Given a little salt and enough time, those plugs can become very hard to remove and in general you'll get corrosion and loss of chrome in any area where salt water is held against the surfaces.
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So...rinsing is a good idea, and soaking in warm water can be an even better idea if the salt has already dried on the regulator. The devil however is in the details.
The safest way to do a rinse or a soak is to do it while the reg is pressurized. A rinse can be done while it is still attached to the tank. Soaking with a large tank is problematic, but you can use a small pony bottle pressurize the reg, and then soak the whole thing in a tub or 5 gallon bucket of water.
Soaking also lets you do a thorough bubble check after each dive. An hour or two is plenty however and over night is over kill as you're leaving the reg under pressure with the knife edge on the first stage orifice pressing on the seats for much longer than your actual dive time, increasing the wear on the seat all out of any proportional benefit of a longer soak.
If you don't rinse with the reg on the tank and/or don't have 6 or 13 cu ft tank, you can still get the benefits of a rinse or a warm water soak, however you need to:
1. ensure that the inlet fitting is tightly sealed.
On a DIN reg, you want to ensure the DIN cap seals against the O-ring in the first stage DIN fitting - not all DIN caps do that.
On a yoke reg you can use an 0-ring sealed cap, or a smooth surfaced rubber ball of appropriate size. Some caps are in effect a rubber ball on a tab that secures it to the yoke screw. If you use an o-ring sealed cap, you want it to be snug enough to seal but if you over tighten it you'll crack the cap and let water in. With a rubber ball you need it to be tight enough to seal, and you need to make sure there are no rings around it (caused by the rubber taking a set in storage) that might let water leak past the ball.
Regardless of what you use, be sure it is dry before you put it on the inlet. Otherwise, you're just moving water into the reg a couple drops at a time. Most of it will be caught in the inlet filter, but once you get salt accumulating there, you are both obstructing gas flow, and if there is any moisture in the gas, you're moving that salt downstream.
2. ensure that the purge buttons are not depressed at anytime during the rinse or soak as that will let water into the system. Swirling the second stage in the water can depress the diaphragm and in turn the lever, opening the system, so you also need to avoid that. And, you don't want the second stage to enter the water diaphragm first (mouthpiece up) as that will also press the diaphragm inward and allow water into the system.
Number 2 in particular illustrates just how careful you need to be to prevent water from entering the low pressure hoses, where it can find it's way to the first stage.
At a minimum, you need to ensure the first stage remains above the second stages during the rinse or soak. When drying the reg, you should hang it by the first stage, so that the second stages are lower. If you have a feature that allows the purge button to be depressed, using it will allow any water in the hoses to drain.
However, the best approach is to re-connect the reg to a tank and then purge both regulators to flow a couple cubic feet of gas through the reg to remove any water that may have found it's way past a seat or seal, and dry out the inside of the second stages as well.
Now there is a piece of wood over the reg rinse spot at the dive shop. First stage must now get rinsed only, no immersion at all. It hangs on the wood and the second stage and octopus get immersed. The reason is that the dust cover may let in water.
Despite all the risks of water getting in the first stage, not rinsing the second stages is a really bad idea as they dry slowly inside and the salt and moisture will corrode metal parts quickly, and cause salt deposits that can interfere with proper function and make servicing difficult.
Consequently I think the intent of the second stage only rinse bucket the OP mentions is to both keep the first stage dry, and to keep it above the second stages due to all the ways water might get in as discussed above.
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However, despite the naysayers who think it's overkill, the ideal method of rinsing or soaking a reg is a combination of keeping the reg pressurized during the rinse or soak, followed by flowing some air or nitrox through the reg afterwards to remove any water that may have intruded and to dry out the second stages before storing the regulator. If you can't rinse or soak it on a tank, you at least should run some air or nitrox through it afterward.
