Learning it is also kind of like learning physics in high school. After a few years you realise the first things you learn are a bootstrap to get started and not actually used in daily speech. Simple example: You hear the words "anata" ("you") and "sayonara" ("goodbye") one time in a month, but you will use them all the time in beginner Japanese class.
"I eat beef" is not something many native English speakers would say, or only in unusual contexts. We may say, "I am a beef eater" or simply "I like beef". Something about "I eat beef" as a statement conjures chest pounding imagery (it sounds primitive), so I'd propose we often pass through a sort of politeness filter too?
Anyways as a English only programmer, I don't know if I learned anything from the article - maybe you have to speak Japanese to get it?
(English grammar being simpler in this trifecta, but then in exchange you have the crazy pronunciation learning of English that I found out I would never "fully learn" and nobody really does in English, since you even have literal competitions (spelling bees) where people show off how good they are at it, and with jokes still happening between professionals like "is it 'data' or 'data'?").
Depends on the manga you read. There are plenty of manga revolving around everyday life, so called "slices of life" by the Western fans. I'd say they tend to use your regular everyday Japanese.
I said/meant that the Japanese learned at school, the one used by people everyday and the one at mangas are 3 different versions of the same language. I still do agree with what you say though.
You can do the same exercise as the author with almost all languages, the only small advantage of Japanese and more programming-like is the combination of kanjis to make up new words but even then the pronunciation might totally change. For example in Spanish:
"I eat beef" = "Yo como ternera" = subject + verb + object. Both in Japanese and Spanish, but not in English, you can omit the subject "yo"/"watashi". But this is so syntetic that people wouldn't use normally, I might instead want to say how good cow meat is and say "¡me encanta la ternera!" "Gyuniku ga suge ski!" (transliterated), in Japanese effectively eating up some random letters there.