Wait I'm confused. Isn't she your sister no matter what?
You can keep this fact from her, which I assume keeps her as your lover on the next planet (At least until Savin makes her figure it out on her own, the bastard).
You mean Astra? Amara is Pirate Boss lady and Astra's father. Not "gross" for that combo.
Waifus are a dime a dozen, but Shade is the only sister we know of.
Yet... who said we not meet down the lane of progressing game some more of our dear papa lost children ( ͡° ͜ʖ ͡°)
And well as OP asked it's easy to get...just picking Lover path for Shade so she will be lover and still sister since latter not chaning only former can be decided by PC actions ^^
*Steele
But yes, intentional.