Nothing in home audio is transparent. Everything affects how a system sounds, including internal wiring and external cables. It is the degree of impact and significance resulting from those differences, as well as the cost, that seems to be most often debated here. To your original point, I agree with you, people can't have it both ways....those who hear differences between different cables and then use those cables to adjust the sound of their system to their liking are using cables as a form of non-adjustable tone control.
If Cables Are Not Tone Controls...
I can't count the times audiophiles have said "Cables are not tone controls". But if we audition (remember that?) two sets of speaker cables and decide that one sounds "better" than the other, aren't we using it as a tone control? You can call it whatever you want, but in reality we are deciding which cable contours the sound to our liking? Or should we just buy the speaker cable with the lowest resistance, inductance and capacitance we can find and if it sounds like crap, change other components until it sounds good? Then we're just using the other components we've swapped out as tone controls. Just asking.