What I think the article misses is the versatility of the traditional music notation’s nature (it misses this by brushing over enharmonic equivalence of flat and sharp notes). It is actually a major helper in understanding musical structure of western music, as it makes the function of certain notes more transparent.
The other aspect that I would like to urge anyone to understand, who wants to understand music theory is the role of intervals and keynote. What tones make you feel that something needs to be resolved, what next tone would resolve the tension.
This is great. I’m in a similar boat where plain memorization never does it for me. I can remember some theory for a short time, but then forget it later. I think I may duplicate this effort in a different language for the sake of understanding it myself.
Music theory has a lot of resemblance to other topics like math, in the sense that there are formalisms at work, however, don’t try to formalise it in a mathematical fashion. Rather, accept the quirks of traditional music notation and work with it (it’s really optimized for that kind of stuff).
Then start by looking at melodies. If you play piano, chose C major and play melodies. Identify which notes feel like you can rest on them for a bit, which notes would feel rather awkward to stop playing (because something needs to be resolved). Look at the intervals and try to get a feeling for them. Don’t try to decouple listening and theory, they need to go hand in hand. Always listen to the stuff you read about by playing it on an instrument.