Ok, let's...
Is Uncle Ben referenced in every single Spider-Man comic in order to constantly remind readers about Spidey's origin?
No.
Does the lack of constant references mean that he "may as well have never existed?"
No.
Just as the vast majority of Spider-Man comics don't feel the need to refer back to Uncle Ben, so too can the movies assume that viewers are already familiar with Spidey's origin and not belabor the point.
Again, in the comics, Peter is not shown to be constantly suffering inner pain or guilt over the past.
Typically, he's guilty, confused or angst-ridden over current problems relating to his love life, or school or work. The Holland Spider-Man films have followed suit with that.
The Daily Bugle doesn't play much of a part in the current comics either. In case you hadn't heard, newspapers are not the most cutting edge thing anymore.
It's been ages in the books since the DB figured prominently in the comics. If the comics are moving way from it - and they have been for at least the last ten years or more - it makes little sense for the movies to entrench Peter in that world.
For years, it made sense for Peter to have a job as a freelance photog. Today that's such an antiquated thing that it would be a mistake to anchor the character to it. The Raimi films were the last time that it made sense for Peter to hold down that type of job.
As for Peter's suits, we've seen his homemade costume, it was what he wore in the climax of Homecoming and it was glimpsed in Civil War so "all his suits/tech" aren't made by Stark or Stark Tech.
It's just that it makes more in-story sense for costumes that look the way his comic costume looks to come from another place.
And there is precedent in the comics with Peter's Iron Spider suit to use Stark tech so it's not completely a fabrication of the movies.
As we saw in Far From Home, it looks like we were moving towards Peter being more hands on with the creation of his suits and tech.
Mentoring someone isn't "belittling" them. There's lives at stake, including Peter's own. If Tony has to be stern when the consequences of mistakes could be catastrophic, so be it. And Peter does make many decisions on his own. That some of those decisions come back to bite him is only being true to the character.
He still lives in Queens with May. It's not like Stark moved them into Avengers Mansion or bought them a house.
MJ knows who Peter is in the comics and has always known (even if that was a retcon) and while she was smart enough to figure it out for herself in the movies, how is that a bad thing? Should she be an idiot who can't see what's right in front of her?
As for Aunt May, she hasn't been frail in the comics for ages. Even her current illness has not made her "frail."
May spent decades on death's door but by the 2000's became a much more active senior citizen. And as for being "an attractive middle age woman", people age much differently than they once did. Back in the '60s, May was probably meant to be a woman in her 50s and no one would find it odd that she looked that decrepit. Today, Jennifer Lopez and Jennifer Aniston are in their 50s. May would have to be pushing 80 to look like the frail old woman she used to be depicted as.
It wasn't. Different aspects have been emphasized or de-emphasized but all of it has its roots in the comics - both from the 616 and the Ultimate U.
Watts clearly knows the character quite well.