I feel its a bit of a stretch. As stated before, RD is no longer canon so why make a totally new ending for the sake of referencing a game that Kato himself felt was so bad he purposely shot down the idea of having it as an extra for the PS1 port?
(SPOILER)
The new ending actually reveals why we don't see Magus cause he doesn't even know who he is anymore and god knows what timeline he even got dropped into. Not to mention the Dalton fight fills the gap of what happened to Porre. It all consistently points to filling in the gaps that Cross created.