It doesn't look like Mahiri skipping grades had anything to do with Mahiro's becoming a hikikomori. She's starting high school here at the same time as Kaede, so she hasn't skipped any grades yet, but Mahiro's already refusing to leave his room. This suggests she skipped grades to get into college early so she could start researching the gender-changing drug to help her brother out. That's some hard-core sisterly love there, and doesn't really appear to be romantic in nature.
The good news is it appears to be working, Mahiro's enjoying his new life as a middle school girl. He has friends, he leaves the house for things other than school, and he seems happy.