Twenty five years of competitive fishing experience has a way of making you come up with "rules" although I would prefer to call them "practices". A good captain always puts "practices" in place to keep problematic things from ever happening again.
You know, like the "cool" practice of riding around with all your rods in the rocket launchers and rod holder. Looks cool until your loose a couple of rods over the side or you run your boat under a "low" bridge at "high" tide with the rocket launcher full of rods, in plain site of about 50 people sitting at the bar in the marina, and proceed to break every one of them in two. 
I bet he put some "practices" into place after that episode.
Back to your beer question. If you've ever experienced the cluster @#$% that goes on in the back of the boat when you have multiple big fish on at the same time you would understand why you don't put drinks on the rail or would want to take a rod holder out of use by using it as a cup holder. No rule against it, just common sense.
Guess the boats that I have fished off of have been very different than your experience. Even with 4 tuna on at the same time, I still need a place to put my beer. lol Although, as already said, I would sacrafice a few spilled beers to catch a few tuna, and have. I'm sure just like anything else on a particular boat, there not for everyone. But I do like them, and will be adding a few to the boat to be an addition to the rod holders already aboard.
These will also be great for those days of just chilling out and relaxing. Not to mention when your jigging etc. Since my boat is only about 28 ft LOA, Anything that does two different jobs on the boat is a good thing.
If you notice, the first pics I posted, the boat owner opted to put another rod holder directly behind this one. It doesn't have to be a replacement for the other rod holders and depending on your trolling set-up it could come in handy set up this way.
