If we consider the prefix counts from Waves 1 through 5 we are currently at +2 Wii tracks, -1 GCN track, and -1 SNES track. The rest of the games are all consistent on the number of prefixes they were assigned vs. what we got. (N64, GBA, DS, 3DS, Tour, nitros)
Wave 6's prefixes were originally:
2 cities
3 nitros
1 GCN
2 Wii
So far the cities and nitro counts are consistent, and unless the final nitro became cut content from Tour then we can assume those will stay the same. Similarly I think Wave 6's GCN slot is safe.
So if we decide to fix the deficit caused by the 2 Wii tracks then that means 1 extra GCN and 1 extra SNES track for Wave 6 to fix the totals. The SNES track is easy to justify because in Tour they remade SNES Bowser's Castle 3 in a big way with sections that scream anti-gravity, and it's like the 1 SNES course in Tour that isn't completely flat terrain.
Justifying the bonus slot for GCN is a lot harder because that means giving up Wii Rainbow Road (the original prefixes had the final track of the BCP as a Wii course and there are no other RRs left in Tour) for the sake of either Mushroom Bridge or the remaining GCN jungle track that didn't occupy the first slot.
If Tour still had GCN tracks coming like GCN Rainbow Road or GCN Wario Colosseum it would be easier to justify, but as it is I think the most reasonable conclusion to take is that a GCN track was replaced in the BCP with an additional Wii track.