No, It's the other way around...DMC3 OUTRIGHT CONTRIDICTS DMC1 and the novel. Plus Capcom has said still that the DMC1 and 2 novels are canon. However...notice I ALSO explained how you can still see there is not actual conflict as far as "it's been this long since you lost your brother"; Vergil hasn't been the same person since. They never actually said that Dante hasn't seen Vergil AT all since he was 8, or at least, the games ndon't specifiy this, especially since in the Novel, he didn't even have a hint that Gilver WAS Vergil until the very end. DMC3 still fits this, in that Dante DID lose Vergil when they were 8, and even the Manga covers them remeeting knowing the other. In essence, yes, the WRITERS cause the issues, but some of them are not as bad to explain as you seem to insist.
And you can expect that Trish had to play dumb to some information per DMC3's retcons that she didn't know about Temen Ni Gru or what really happened. You really think Mundus told her everything?