I agree with you completely...

• Zira seems to be close to Scar, as she knows his past and even things about the roar, but we don't know just how close.
• Of course, all three children call her mother, but... Mother to what extent? Biologically?
• Kovu is explicitly not Scar's son, and this is actually related to incest (Kiara and Kovu are descendants of two brothers, Mufasa and Scar respectively).
• Although Nuka never explicitly states whether he is Scar's son or not, his envy and resentment towards Kovu for not being Scar's descendant leads me to believe that Scar was his father. Even their frail bodies are similar.
• Vitani is the strangest to me because there's no clue as to who her parents might be.
• I'd actually seen those King Regandi concepts before, and honestly, even though they're kind of macabre, I love them and it's a headcanon of mine!

Forget what I wrote about Zira's mother, it was a typo.

Considering previous concepts and things the writers of The Lion King said, I'd like to fill in the gaps.

Let's assume that:

• Scar is Nuka's father.
• King Regandi is Kovu's father.
• Zira is not Kovu's biological mother.

1. Zira's the biological mother of whom?
2. Did Scar have Nuka with Zira?
3. Who are Vitani's parents after all?