I don't see that at all. It is the literal translation, but it isn't right in English. This comes from the fact that English and Portuguese do not use the tenses in exactly the same way. You simply can't say "we are friends since..." in English (maybe in some colloquialisms, but it is definitely not good enough English to learn).
I dont think at this level they are concerned with the translation of the sentiment if the sentence, rather the words within the sentence. So, while it wouldnt be proper grammar in english, it would be poor teaching technique to mark it as wrong. That would be something to worry about later. So, that's probably why they are accepting "We are friends since yesterday" as correct now.
One of the functions of the present perfect tense is to describe an interval of time from the past (yesterday) until the moment of speaking. The Portuguese "simple present" focuses only on now, not the past.
We are friends [today]. (Simple present)
We have been friends since yesterday. (Present Perfect)
Honestly, these are living languages - at some point, it is the population that determines what is "correct," not simply only the grammarians.
Sure. The society that uses the language also determines what is acceptable or not. That's why a language is living and keeps changing.
Would it be appropriate in any circumstances to use the Portuguese present perfect in this situation? 'We have been being': 'nós temos sido amigos'? Or would estar be more correct, if used at all?
The "present perfect" tense is what you see in DL's sentence: "have" + past participle = (been).
We have been friends since yesterday, for ages, since 2012...
With a few exceptions, the "present perfect progressive" tense: "have been" + present participle is not used with verbs like "have, like, owe, be, seem..." The simple present perfect is used for this type of verb.
The second timeline shows the simple present perfect tense describing a durative action. (past -> present)