"How come that..." is not good English. To my (American) ear, this use of "How come" sounds like a literal translation of the Spanish phrase "Por qué". This use of "How come" is natural for many American English speakers who are also native speakers of Spanish. It is not natural for most other American English speakers.
Your two examples would sound more natural (to me) as:
How did you learn to speak English so well?
Why do people eat hot food in hot countries?
I think what the page meant by saying "when, where, who" is that the perfect form doesn't go well with expressions suggests a particular time. The example sentences given at the linked page seem to be all about it.
The default past tense is the simple past, as Michael Swan says in his Practical English Usage (§421.4 "In general, the simple past tense is the ‘normal’ one for talking about the past; we use it if we do not have a special reason for using one of the other tenses.")
The perfect forms are needed basically to add the sense of completion to non-finite verbs such as infinitives, participles, and modal verbs. Because such tool exists, it's also used to talk about past events, but it ends up saying 'up until now' ('up until sometime ago' when it's the past perfect). Because it's tenseless by itself, it makes the sense of time vague, thus it has the sense of duration at the same time it conveys the sense of completion.
The use of the perfect forms are more to do with meaning than tense. Grammar books usually says it's one of tense form, but actually it's not about tense. Linguists call it 'aspect'.
The perfect form goes well with expressions like already, recently, just, since, ever, never. But it doesn't go well with expressions of particular point of time, when, such as yesterday.
I've read something more relevant to the OP's question, in the same M. Swan's PEU:
§457.1 (...) we usually prefer a past tense when we identify the person, thing or circumstances responsible for a present situation (because we are thinking about the past cause, not the present result). Compare:
Look what John's given me! (thinking about the gift)
Who gave you that? (thinking about the past action of giving)
Also
PEU §456.5
We normally use the present perfect to announce news. But when we give more details, we usually change to a past tense.
There has been a plane crash near Bristol. Witnesses say that there was an explosion as the aircraft was taking off, ...
Best Answer
This is atrocious English
But you're correct, it has become common in colloquial speech, especially among some subcultures. The tendency to drop the verb "to be" and its counterpart behavior, the tendency to never conjugate the verb, stem from U.S. subcultrues in the 1970s, which were derived from the "Jive" lingo from the African-American jazz culture of the 1930s and 1940s. Both behaviors are ungrammatical (unless the world today has decided to become accommodating, language is fluid).
An example of dropping the verb comes from the 70s popular TV situation comedy, "Diff'rent Strokes."
An example of not conjugating the verb comes from a more recent experience. While helping a friend prepare to test for his commercial driving license, he would chant through the pre-drive test and check procedures like this: