You dont need to look at the interview which is muddled and terrible. You need but look at Other M. Samus states in Other M that it's her first time doing a joint mission with the Galactic Federation since becoming a freelance bounty hunter. This obviously ignores the Prime series via in game dialogue. Or Monologue. Whichever.
It goes on further throughout the game making various nods and references to the rest of the series, except for the Prime series. It would stand to reason that, while not directly saying that isn't in canon, that they don't want it to be apart of the timeline. Even in the proper translation of the interview Sakamoto states that "Nearly everybody has asked about the Prime series, which are part of the Metroid timeline, but are completely different." What does "completely different" even mean in this context. No one knows. Even if they are not decanonizing it, they are at the very least trying to shy away and make people forget about it. Much like the CD-i stuff and many other perceived misuse of the Big N's toys.