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We know that Phineas and Ferb are step brothers. It's obvious that Ferb has head shaped just like his fathers'. Is Doofenshmirtz maybe Phineas's real father since they have very similar triangular shaped heads and they are both very creative and inventive?

There were also some hints that Doofenshmirtz was with Linda.
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Is there any in or out universe explanation about this?

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Very unlikely. We only know about one date which didn't even end well:

Doofenshmirtz then tells him about one of his first dates. It was with Linda Flynn and they were in a drive-in theater, going to watch a film. Linda says that she would like to be a pop star one day. Doofenshmirtz sarcastically replies that he will take over the world, and she suggests that he should start small and try to take over the Tri-State Area. Doofenshmirtz says it's unlikely but he'll try. He then brings out a machine to make the movie's sound 5th Dimensional and attaches it to their car. Unfortunately, the machine makes the cinema screen explode and blast off into the sky. Whilst finishing his flashback, Doofenshmirtz trips on one of his traps and knocks his latest machine into the Flynn-Fletcher house in the front lawn. - phineasandferb.wikia.com

I don't think in one date he can father two children and it didn't even end well. From wikipedia:

Phineas's birth father is never present or discussed in the series, something Marsh and Povenmire have stated that they fully intend to keep that way.

Same applies for Ferb's mother too. We don't know. Fans can make any theory, but the creators want to keep it in suspense.

And many sources/people (1, 2) claim that creators have denied this theory.

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Another thing detracting credibility from your theory is that not only is the head-shape thing not shown to be hereditary in-universe, but Phineas Flynn and Heinz Doofenshmirtz also have different variants of head shape. Phineas, for example, has a long pointy nose, while Heinz has his chin as the point of his triangular skull. With such wild anatomical differences, it's a miracle they're even the same species (actually, legally speaking, they're not!).

I'd also argue that though Phineas and Heinz both seem to be master engineers, that's maybe the only quality that the two share. Heinz is a classic screwball with a fractured childhood, unconventional relationships with others, and deep, unresolved animosity. Phineas is a curious, inventive, optimistic boy for whom life seems to be a world of pleasure - he's rarely ever seriously upset at anything.

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