MAJOR verb tense confusion - how to correctly use past perfect in a past tense narrative

Okay, scenario: In a novel set in narrative past tense, there’s a sentence, "We had become friends when nobody had liked him and it had seemed no one ever would." Is the past perfect being used correctly? Is "when" perhaps too ambiguous and unhelpful?

To my mind, there are three different times here: 1. the "now"; 2. the moment the boy and girl became friends; 3. the time when the boy had no friends. Put like that, the solution seems simple–use past perfect for the time when the boy had no friends because it occurred before the moment he and the girl became friends. E.g. "We became friends when nobody had liked him and it had seemed no one ever would."

However, because the novel is already set in past tense, I’m afraid using past simple for the moment they became friends, which is in the novel’s past, would get confused with the "now," which is also written in past simple. So is it more appropriate to use past perfect for both past events, even though they didn’t occur at the same time?

In that case, are all three hads necessary, or can it be used with only the initial verb (became) then understood to also apply to the two others (liked, seemed)? E.g. "We had become friends when nobody liked him and it seemed no one ever would." I swear I see that in novels all the time, but I can’t find any sources to confirm it’s a thing. Maybe that’s a misconception on my part. Or maybe it’s just super common to misuse past perfect.

Help 🙁