I think if people come off with that impression it's because Tony's presence and impact go beyond his physical appearances.
He's as pivotal a factor in Peter's Superhero side as Liz is to his civilian side.
I mean, yeah, but it's much more felt and really illustrated in certain adaptions over others.Whether it's directly stated or not, May is always the most important person in Peter's life.
I won't disagree he's had surrogate father figures in his life, but making them a Superhero certainly changes the dynamic a lot (and not for the better in my opinion).That's debatable, of course. But the larger point being that Peter has historically had surrogate father figures in his life. Especially early on. So it's not unusual to see that represented in the MCU. It also doesn't preclude the importance of women in his life.