Couple of things:
1. The problem is present in all five films and not just in FFH.
2. It is inaccurate to say that Peter misses Iron Man the Superhero and not Tony the person, or that he unblindly looks up only to the Iron Man part of Tony, when he's had a personal relationship with Tony for four films and explicitly states he misses him.
3. To the extent that FFH and Homecoming acknowledge that Tony made mistakes, it's only in the broad "all humans make mistakes" sense. As if Tony's mistakes are on par with Steve Rogers'.
4. The overall context is what's most problematic about the Tony worshipping. The two villains he indirectly created aren't treated by the films with the same leniency and "all humans make mistakes" type of attitude. The effect of this is that the films give off classist undertones, whether it was intentional or not.
5. Even when Happy gives Peter the speech on how Tony wanted him to be better, it's in the context of Tony choosing him over everyone else and how Peter should be honored by that. The film never abandons the classist undertones in Tony and Peter's dynamic.
6. FFH specifically sends very mixed messages. The scene where Peter supposedly established his independence is followed up by Peter doing science in Tony-style and Back In Black playing.