The problem with color codes that actually makes them dangerous in practice is that a number of people who practice them do not do so because they have carefully designed a system for safe gas switches using them, but instead because they happened to have a green stage regulator for their oxygen and their gas switching procedure abbreviated over time until it was just the color code, without paying the amount of reverence to placing a regulator on a tank that such a system requires.
In my view, it seems like dedicating tanks to a purpose is by far the more flexible option. There's a lot less value in being able to replace your 80CF bottom stage with a 40CF bottle usually used for oxygen than there is in being able to replace your bottom stage regulator with the functionally identical regulator usually used for oxygen. Furthermore, problems with regulators are more likely and wider in variety than problems with tanks, so it's still better to be able to exchange regulators even if the cylinders could be exchanged freely. Also, in the event that it is necessary to re-designate a cylinder, it can be done in a pinch with duct tape and a sharpie while re-designating a regulator would require having a properly-colored faceplate in your save-a-dive kit. Finally, a labeled-tank system theoretically scales better if you need a huge number of gases because there's only so many readily-distinguishable colors. For these reasons, it is my opinion that dedicating bottles is the better system unless one has an unusual logistical situation that makes those trade-offs weigh differently.
With all that being said, I am not convinced that it impossible to develop a system that is safe and relies on color codes. I am guessing that color code systems evoke such a strong response because many people have seen someone that pretty clearly relaxed into a (bad) color-code system out of complacency while it's relatively uncommon (at least in my experience) to see someone using a structured, well-thought-out color code system. Despite all the real issues it causes with convenience, the fact that you can physically attach a regulator of the wrong color to a cylinder does not seem to me to be any more of an inherent safety issue than the fact that you can physically fill a cylinder with a gas it is not labeled for.