Takanuva's journey through a bunch of alternate universes in 2008 is just a way to explain away his set tools, shoehorn in some "what-if" scenarios, and tell a few side stories. Seriously, they could just as easily have had Helryx give him his new weaponry. It also makes no sense that he stumbles around through these universes and somehow magically winds up back in his own -- in Karda Nui, no less. However, it could have made sense if the order of the three stories was rearranged.
Canonically, it goes
City of Silver
Here's the order I propose:
City of Silver
(and the only thing this would affect is any mention of weaponry in Dark Mirror, if there was any, which I don't think there was)
Brutaka uses his Olmak to send Tak to Karda Nui, but his Mask is damaged and winds up sending him to an Alternate Universe instead -- still on Metru Nui, though, where he started. At the end, he jumps into Dimensional Space, no control over where he's even going, and winds up in a pocket dimension.
After helping out here, he describes his universe as best he can to the Spectral Hau, who knows nothing about his universe. The SH sends him to a similar universe.
Here, the only difference is that Matoro failed (and Velika wasn't a GB, but no one cares about that). After helping out here, Tak finds Brutaka with a working Olmak, who knows how to use it, and Brutaka sends him exactly where he wants to go.
Again, I stress that this would do nothing to the continuity, since there wasn't much mention of his weapons in DM and his weapons in Journey of Takanuva are creative license anyway. What it would do is make the whole journey actually make sense. It would have made more sense if they had just cut this whole thing and had the OoMN give him his new weaponry, but if they really wanted to show these stories, this is how it should've been handled.