I read the article and it is fairly informative, but it does not support the conclusion that because human hearing is non-linear tone controls are a must.
From the article: Let's consider the facts, not hogwash peddled as audio wisdom. The article isn't total hogwash, but is an opinion and a convenient misinterpretation of the facts to make them fit with the premise that 'tone controls are a must'.
1. Tone controls exist on the premise that our hearing is non‑linear, a fact proved so many times it's a waste of time proving it again.
Hearing is non-linear is a fact - they even provide a nice Fletcher-Munson chart as supporting evidence, but say So far, we have subjective differences of sound perception due to volume levels, which is NOT what Fletcher and Munson proved. Subjective differences in sound levels only come into play when you consider that my ears may be different than yours. As cited in the article, the author has a small suck out in the 5-9kHz range and thus he might benefit from boosting that range. I have no such impediment and wouldn't benefit from a boost in that range. Both of our ears are still non-linear.
F&M proved that our hearing is less sensitive in the very low frequency range and the very high frequency range - meaning that in order to perceive a low bass frequency or a high frequency as being just as loud as a frequency in our most sensitive range, it must be at a much higher amplitude.
From the chart:
In order for us to perceive a 100 Hz tone at the same loudness level as a 1000Hz tone, the 100 Hz tone must be at 40 dB when the 1000Hz tone can be at 0dB (the threshold of hearing - not silence). Likewise, at 10 kHz the tone must be close to 20dB.
As you can see using the bass tone control to boost a few decibles isn't going to do squat to overcome the non-linearity of the frequency response of the ear.
2. a. Next come our loudspeakers. Theoretically, they are linear, but in practice, they are far from linear all on their own.
b. But speakers have many other problems, one of which is the room we sit in and listen to music. Depending on its size, proportions, furniture and furnishings in general, it WILL interact with the speaker, there are no two ways about it.
c. Then there's the music material. If you like a particular recording but feel it's too dark, or not coherent enough, what will you do about it?
Not exactly earth shaking revelations. The room, speakers, source material, and electronics all affect the perception of sound. Tone controls are a very crude tool to use to overcome all of those obstacles because they affect a single bass frequency or a single treble frequency. An equalizer can be used to adjust more frequencies of course, but without a skilled operator they generally make things far worse. The best solution is to treat your room properly to eliminate the problems in the first place and then maybe use tone controls for fine tuning.
Remember, the column is entitled 'Views & Opinions' and that is all it is despite trying to fit the scientific data to support the opinion. The only opinion that really matters is your own, so use the tone controls if you like them.