I don't think that the writers / developers have thought about it. I mean, in DMC1 when you hear Dante's thoughts of Vergil, it's about him as a kid with Vergil. But, in my opinion, the only reason we hear that is because the events of DMC3 had not been thought of at that point. If they had planned ahead, they would have had Vergil's adult voice in Dante's head surely. It might be argued that Dante's memory of Vergil is mainly childhood... but the last time he saw Vergil was pretty intense, and you'd think that would be his strongest memory of him.
I haven't seen any official confirmation about Eva's relationship with Vergil, so I wouldn't believe what it says in the manga necessarily. However, just by speculating, it might very well seem that way to Vergil even if it wasn't true. Maybe Vergil is just insecure or unhappy generally, and so he would feel paranoid that he was unloved by his mother, and would interpret it that way rather than be optimistic.