I like most of what you said with one exception. You mention a "friend" who thought marking queens allowed him to control his genetics. But that leaves so many possibilities open. Was he a breeder? Of course marking queen could be used to control genetics by knowing if you have the same queen in your yards, drone support yards, and so on. Controlling genetics by solely relying on some idea that marking queens does this alone, may be wrong, but yet can be a vital part of control in regards to keeping track of queens.
If your friend is a hobbyist, and want to run a certain queen, say some hygienic line from some particular breeder, then also knowing if that queen has left and replaced can also be helpful. While most hobbyists are not going to replace a queen everytime a new queen appears without a mark, there are some that do.
Now don't get me wrong.....I do not mark queens. And I do not promote to others some management item that may or not be harmful. And why some take some hard fast approach of preaching to others some idea that beekeepers should do this or that, such as marking queens, when it makes no impact on their own operation or affects others, is a bit amusing.
Some over the years have suggested that marking queens increases supercedure, and a host of other problems. And it is funny how "pro-Marking" advocates point out some slim angle of the idea that emergency queens, or some other reasoning, yet fail to acknowledge how many folks do just as much damage marking queens, by having them fly away in handling techniques, squeezing the crap out of them in push up cages, smothering queens in globs of paint, and so on. the stories of beekeepers marking queens make some very funny stories, but sad ones at that.
I do not mark my queens due to no single product ever made specifically for this use. I have heard of beekeepers using everything from nail polish to Superglue with painted disks. I called many manufacturers of the paint pens and sought information on the use of their products, and was shocked to find out some of the details. This information can be found here: http://www.bjornapiaries.com/beekramblings200910.html
Read that link if have not done so. Go down to May 2009.
What does the average beekeeper do when having a marked queen? They go into the hive, with the sole goal of seeing that glorious queen. The moment they do, they get a warm fuzzy feeling, the world seems right, and they end their inspection. And many would be better knowing that even if you don't see the queen, you are missing about 95% of what a hive can tell you about health and problems. If you verify that a queen has a good pattern, you find fresh eggs, then how many are going to kill that queen as mentioned earlier for the sake of a missing mark? Not many.
Mark...don't mark.....in the end, it is just the individual beekeeper fooling themselves many times.
Except for the reasoning of control in AHB areas, I see no real reason to promote marking queens on a wide industry scale. Some individuals may find use, but those that push, push across the board. They have taken a stance years ago, made a name for themselves in taking certain stances, and will continue to do so till the last days.