Is Doof Phineas' Father?

No- Evidence:

Givens

The Star Wars episode is not part of canon as the characters do not seem to match their ages in the show (Candace leaves home before their dad leaves and before Ferb joins their family, which would be at age five if their age was the same)- 46:45

Flynn is Linda’s maiden name as her parents and sister also have the last name “Flynn”

Every occasion where Phineas has interacted with Doof as been erased from his memory (Night of the Living Pharmacists, Into the 2nd Dimension) except for the new movie

Witnesses

Heinz Doofenshmirtz: has professed to only meeting Linda Flynn once, supposedly fathered Vanessa Doofenshmirtz, previously married to Charlene Doofenshmirtz but on good terms with, arch nemesis with the Flynn family pet and OWCA agent Perry the Platypus

Linda Flynn: former one hit wonder popstar- Lindonna, mother of Candace and Phineas Flynn, stepmother of Ferb Fletcher, wife of Lawrence Fletcher, friend to Charlene Doofenshmirtz

Candace Flynn: never knew her father, was alone when Linda returned from the hospital with Phineas, has met Heinz on multiple occasions and just refers to him as “Vanessa’s dad”

Norm: works for Heinz, has a robot does not have the capability to lie, admits to Heinz that Linda does not remember him

Charlene Doofenshmirtz: ex-wife of Heinz Doofenshmirtz, casual friends with Linda, mother of Vanessa

Evidence

Timeline: Linda and Heinz dated once in the 70s, she met Lawrence in the 90s, Phineas and Ferb were toddlers- about 2- when they met, at the time of the TV show Candace is fifteen and Phineas and Ferb are about ten suggesting they are about five years apart

The Date: (S2 E19 2:40, S3 E35 15:00ish) Doofenshmirtz himself admits on two occasions that they only met that one time and that he never saw her again after that, Linda despised him and clearly asked to be taken home within ten minutes of their arrival, she was forced to ride in the trunk of their entirety of the drive there.

Canon: The creators of Phineas and Ferb have confirmed that neither Doofenshmirtz nor Pierre the Pinhead are Candace and Phineas’ parents.

Interactions (S1 E12 16:47, E4 S33 8:24): Charlene and Linda are casual friends- if Heinz was having an affair neither of them knew about it (Charlene said they split amicably), Candace knows Heinz as “Vanessa’s dad”, Phineas hasn’t reacted to Heinz as anyone but a pharmacist weirdo in special episodes

Traits: don’t share agreeableness, consciousness, extroversion, neuroticism, they do share openness

Aesthetics: Both Candace and Phineas have red hair, suggesting their father also had red hair or had blond hair since “red” is a recessive trait.

Candace has a long neck like her mother and grandmother and a face shape similar to her grandmothers’. She has red hair like her mother and a weak chin like her grandmother

Phineas has a very defined triangle head with sharp 60 degree angles that have not changed since his birth. He has more “red” hair than Candace (closer to his mom’s color than Candace’s) and does not have a chin. He has small ears just like his mother and grandfather.

Doofenshmirtz has a soft angular-shaped head that becomes more “triangular” as his chin grows more defiant. He has a very strong chin and a very large nose, which every Doofenshmirtz (except Vanessa- more on that later) also possesses. He has light brown hair similar to his parents and brother, Roger and small ears.

Unlike Doofenshmirtz, Phineas has had his unlike head shape since he was born. Also unlike other characters with angular shaped heads- Doof and Thaddeus- Phineas’ head is pointed out as odd shaped, meaning it is NOT normal in their fictional world to have a head as triangular as Phineas’ (S4 E11 6:06). Thaddeus is the only character other than Phineas to have such a sharp angle in his head. Doof’s head shape is more of an isosceles right triangle while Phineas’ is an equilateral triangle.

Candace also does not seem to possess this triangular head gene or at least it is a very recessive trait as none of her kids have this shape.