For TV Vs. DYRL, yeah...i remember an interview in Animag where Kawamori said that both were equally valid, but that was before Studio Nue came up with the timeline, so I'm not sure his words still stand.
As for Zero, IIRC, there was a big kerfuffle here about Zero not fitting in with Rainy Night, since he confessed his love to Claudia the night before taking the VF-X-1 out for a first spin, and he was scared because it was different from anything he'd flown before. So we had people trying to rationalize how in Zero, he was flying a variable fighter quite skillfully but was apparently "unattached," if you will.
My answer is that Zero happened AFTER he hooked up with Claudia, but he wasn't expecting to run into an old woulda/coulda/shoulda...and thoughts of Claudia took a backseat. If Aries had lived, he would've had quite a choice to make...
I still think it works better as a pre-DYRL story, though.