Technically, neither Jaye nor Mallory is really "incest" though both situations dance with it. Both relationships make the reader consider, hypothetically, what they would be comfortable with. Could you be intimate with someone you grew up with as siblings, or could you be intimate with someone who is a genetic clone of your mother BUT she is her own woman, she's your age, and has a completely different unique personality and appearance?
It's "No blood relation but she's family" vs "Synthetic Blood Relation and she's not Family"
For me, I'm personally more comfortable with the Mallory situation. I still see Jaye as a sibling character, but Mallory as a more traditional love interest. Mallory and Alex have great chemistry with each other and are falling in love by the time the "clone" revelation came about.
I remember reading a story several years ago in the U.K. about a couple who were married several years and then later found out that they were actually blood siblings. When they found out, they said "fuck it" and didn't let that get in the way of their relationship. On paper, they are incestuous, but they never had a sibling relationship and the love came before the revelation.
If I were in the same situation, I'd say "fuck it" too. If I were to put myself in Alex's shoes, the clone thing would change literally nothing for me.