Well let me say this, there is no definitive proof either way right now. We don't have a Midway stamped letter saying "Only the Warrior came with the N64" version.
However, what we do know, is that the two that have surfaced through legitimate means (i.e. sold 100% complete and not pieced together), both had the Warrior.
We also know that there was a mail away offer with the PS1 / Dreamcast version of the game, that would let you obtain some figurines:
The current theory is that the Warrior is the N64 exclusive. Over time, I believe this will be proven as the Warrior should surface to the top in terms of rarity. I've already seen sets sold or pics of sets missing the Warrior.
People can form whatever opinion they like, but one collector showing a loose figurine with a box (after many loose figurines were sold / talked about over the past weeks) doesn't prove anything. Especially with the tray missing. The tray is either missing because someone pieced it together, or simply because it doesn't even fit in the first place.