A bit of clarification on the 'warped' dungeons. Any dungeon post game with a high 'mystery' level is capable of warping you, and apparently, there are 5 possibilities as listed below. Take note that 6 of the post-game dungeons are special in that, 2 kinds of important 'warps' are possible through them. These are the Quiet Tundra, Dream Island, the Moonlight Forest, Iron Rust Mountain, Large Pit, Smokey Mountain.
1) You get warped to a dungeon with the exact same name, but conditions are reversed (i.e. you cannot recruit the Pokemon there despite you normally could). Similarly, if you originally cannot recruit Pokemon in that dungeon, you could after the warp (applies mainly to the post-game dungeons which are not the 6 ones listed above)
2) You get warped to one of the dungeons that are no longer accessible post-game, for instance the Glacier Palace East and West. This usually happens with the earlier pre-game dungeons.
3) You get warped to the 'Golden Chamber', where there are rare items and different Pokemon listings.
4) You get warped to the 'Mapless Street', which is only possible through one of the above 6 dungeons. The starters are mainly ound here. There appears to be 3 different 'Mapless Streets':
A - accessible via Quiet Tundra or Dream Island, you can find the Pikachu line and Oshawott line here
B - accessible via Moonlight Forest or Iron Rust Mountain, you can find the Snivy line here
C - accessible via Large Pit or Smokey Mountain, you can find the Tepig line and Axew line her
5) You get warped to the 'Golden Chamber Deepist Part', which is again only accessible via the 6 special dungeons. You find Tornadus or Thundurus here. Again, there are 2 different 'Golden Chamber Deepest Part':
A - accessible via Quiet Tundra, Dream Island or Moonlight Forest, you can find Tornadus here
B - accessible via Iron Rust Mountain, Large Pit or Smokey Mountain, you can find Thundurus here
The six special dungeons only takes you to either 'Mapless Street' or 'Golden Chamber Deepest Part' apparently, and you cannot get the other kinds of warps through them. Similarly, the 3 other kinds of warps are only possible in all the other dungeons.
In addition, for the Cobalion and Terrakion missions to appear (which is by random on the right side notice board), it seems you need at least the Royal Rank. A word of advice for Landorus, Thundurus and Tornadus is that, consider using the type based gifts, since the chance of recruiting them without the gifts seem extremely low. Landorus is found on the 8/F of Breezy Plains after the end credits, and my personal experience is that if you can recruit Landorus (with the ground or flying gift), you basically nailed the game. It comes at level 70 and knows Earthquake. You can almost kill anything with Landorus at this point, even the weaker Reshiram and Zekrom who are weak against you. After it learnt Stone Edge, it could easily take out Ho-Oh too. Of course, you still need a few Revive Seeds just in case.
The special legendaries appear in fixed 'challenge' dungeons. According to the Japanese boards, it seems that Ho-Oh is the only one that may appear shiny, not the other ones for some odd reason:
1) Ho-Oh - Eternal Ruins
2) Lugia - Tidal Sound Ruins
3) Reshiram - White Summit
4) Zekrom - Black Edge
5) Kyurem - Sky Tower
6) Black or White Kyurem - Deserted Sky Tower
Coronis~