I don't understand why it's so hard for people to accept, that this girl might just actually be into him.
She's no Aphrodite herself, and I can imagine a lot of bullying could've put her self esteem down. Chris is the epitome of a retarded sperg, but he is kind and healthy, and bears no physical disabilities. It's not like he is a handicapped vegetable in a wheelchair, who needs feeding 3 times a day, and his diaper changed before bedtime.
The fact that Flutter is seeking friendships, online and out of her country, in the first place, is already a major indication that this girl is not completely there herself, and might struggle socially with friendships.
I've followed this thread for a while now, and actually signed up here because of this, and my take is that they are indeed a couple, and that Flutter indeed enjoys the company of Chris.
I didn't know Chris-chan until 2 weeks ago, and it's fairly possible that Flutter didn't either, before she engaged in the relationship. Once you fall for someone, it's difficult to change your opinion on them, and when the world seemingly goes against the two of you, it only helps bond you closer together.