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Painted magazines don't work well if it is dark.
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Too true.
But I have to ask: why would a person put a potentially "wrong" mag with their "bump in the night" gun? I have a bunch of guns in the safe that would not be the first thing I would reach for if something bad were to happen. I have guns for competition, hunting, and just plinking. I have some guns from the same manufacturer in different calibers, as evident from my photo above. But that safe isn't where I keep my "go to" defensive guns.
I'm not worried about getting the wrong colored mag in the gun if I have to respond to a breaking window in the middle of the night. Or if I have to reload my carry gun on the street. Why? Because I don't keep the "wrong" mags with those guns.
Your approach with different base pads is a ligitimate solution, and it sounds like it works well for you. However, it sounds as though your method would preclude you from owning other sorts of other guns. Maybe that's okay with you, as that's not what interests you. And that's okay too.
The answer is to do what you and others have done, which is to think about your individual situation and come up with a solution that fits your needs. Because your needs might not match up exactly with my needs, so my solution isn't best for you, but yours is. And that's okay too.