It comes from the idea that there's an "ideal" Spider-Man IE "Homecoming is the ideal portrayal" but no one knows where that comes from (can't source it anywhere). It's just a combination of features Spider-Man / Peter Parker have exhibited throughout the years. Homecoming and Raimi's versions are quite similar except Homecoming doesn't explore or show Peter / Spider-Man struggle in a meaningful way that connects to the audience. Homecoming prioritized fun over making a character you can relate to more than just "I want to be an Avenger". Civil War set up Spider-Man pretty well (poor, making shit out of dumpster bin shit) but then this just forgets it all. Like, it's a waste of a set up because you don't get any focus on Peter's genius side. Raimi gave you the entire package and people loved the shit out of it. Think of how Raimi portrays Peter's decision to focus on Peter and not Spider-Man, his genius side is shown by him not being just super smart but by being more diligent to his school work / himself which is something A LOT of people can relate to. People love it so much people are actually defending Spider-Man 3 in this day and age.
Since seeing it, I have felt that the Spectacular Spider-Man television series did the best job of capturing the essence of the character. To me, it's similar to B:TAS Batman insofar as it is a distillation of elements from lots of other portrayals (the Raimi films and both Amazing and Ultimate comic book runs) to create a particular take on the character that (for me) is the best version of that character. If you were to ask me about my ideal, that's what I'd lean towards.
I don't agree with your interpretation of the character in Homecoming, though. You see him making his own webbing in the film; you see him working with Ned on modifying his suit; and its clear from other information (e.g. where he goes to school, his position on the team, the respect others on the team have for his intelligence if not his reliability) that he's very smart. So, I don't really know what you mean. I also don't really watch these films looking to identify with or relate to the characters. I didn't identify with Parker during the Raimi films, and I was a few months from 15 when the first film came out, and socially awkward to boot. Don't ask me why I didn't. But for me, the character as portrayed in Homecoming was more sympathetic, at least. I suspect it has to do with the actor; I really, really liked Tom Holland in The Impossible, so I had a kind of preexisting sympathy there, and more substantively I thought he better captured what makes the character charming (in a dorky kind of way) for me.
And I have never seen SM3. I thought it looked uninteresting at the time, and then it was panned so I never got around to seeing it.