Kira is Mrs S' niece, not sister.

"Surely this wasn't just snark at an unwelcome reminder of something obvious that hadn't been overlooked?"

"Summary execution for merely threatening a child is not right, by the way." Sounds like you're tangled in an is-ought problem.

Why can't the Ledas take after their father (who technically isn't Kendall, but is actually hitching a ride inside her, more like Kuato from Total Recall, except only existing just a organ or tissue with different DNA) instead of their mother?

The only way for Sarah to be Siobhan's mother is if Duncan used Siobhan's DNA instead of Kendall's. Clones are just forced twins.

Siobhan isn't Sarah's daughter, because Kendall is a chimera, not a mosaic. Thus, Sarah and Siobhan have different fathers.

A clone is just a forced twin. Not all twins look alike. Even "identical" twins aren't identical. All twins have different phenotypes (outward traits) even if they share the same genotype, because of epigenetics.

Siobhan and Sarah have two different fathers, so Siobhan can't be Sarah's daughter.