Let's get real. Miyuki has the hardest time for being inlove with her brother. It's not even a joke how pitiful she is on what is happening to her life situation.
Miyuki is a modified magician so she was genetically engineered in order to achieve perfection.
Maya told Tatsuya that they (aunt, nephew) are closer related than he and Miyuki. Obs: Maya is his mother's identical twin, their genetic relationship should be the same as mother and son. So idk if she was referring to the usual DNA share between Aunt/Nephew around 25% or their most likely DNA share around 50%. Normal siblings DNA share is usually ~50% and first cousins ~12.5%.
She also said Miyuki would notice she and Tatsuya are compatible because their genetic relationship is 'quite' far. It was not mentioned how far it is.
Tatsuya and Miyuki share the same parents so they are biological siblings, but due to Miyuki's modification their genetic relationship is far however they are still related. Maya affirmed that children between the two would have no issues as all genes that could lead to abnormalities in Miyuki's offspring were removed.