I used to think as you do. In 2009 Boeing had a problem with sticking autopilot disconnect switches. It took considerable effort to identify the problem. These are simple switches that are mounted in the control wheel. It turned out that the flightline guys had lubed the switches with silicone based (Dow Corning DC4) grease and it caused the parts to swell which inhibited movement. The swelling took some time so the problem wasn't seen until the airplanes entered service for a week or two. This wasn't a safety problem (because the switches would only prevent the autopilot from engaging) but a warranty issue never the less. To date autopilot switches are left dry for that reason. Sorry but I don't remember the exact formulas involved.
Back to boat O rings. Use manufacturer's recommendations or risk early failure. This isn't theory and I'm not guessing, it's based on experience and a detailed materials analysis. I'm a 4 years retired Boeing Flight Analyst.
Ken
after doing some research on the Dow Corning Compound4 , which
is a silicone based product, it does have a warning that using it in certain applications can cause seizing....
the DC4 product is not as commonly used by the general public as is the 111, which does NOT carry the warning, and which is recommended by ALL manufactures of SCUBA equipment as the lubricant that should be used when servicing SCUBA components...
Parker-Hannifin, who is a supplier of products to the aerospace industry, only offer two different lubes for seal and o-rings, a lithium based product and a silicone based product... their claim is that silicone can be used on all seals and o-rings, yet in some high volume applications it may be cheaper to use a lithium based grease.
so we have to conclude there may be some special seals used in the aeronautics industry are sensitive to silicone lube, OR... that they are sensitive to the thickening agent that is used in certain silicone compounds. but not at all common in general use.
so you are correct.... not all seals are always compatible.
but hopefully we can agree that we shouldnt be comparing an airplane with a toilet, when deciding what to lube the crapper with

