There could have been a Mystery Gift that made it possible to encounter pineco in the Altering Cave, but there was no event where that Mystery Gift was distributed.
Only zubat can be found in Altering Cave. Altering Cave was a location intended to be used for an event where Mystery Gifts could change the pokemon encountered in the cave, but these Mystery Gifts were never officially distributed.
Squirtles can be found at Lake Afar.
mewtwo is in mystery cave :D
Altering Cave is an event area, but no events for the area were ever held. Initially only zubat could be found in Altering Cave, but a special mystery gift could change the pokemon that could be found.
jirachi is found at the end of wish cave
Forestville Mystery Cave State Park was created in 1963.
Piplup is only found in Pokemon Mystery Dungeon Explorers of Time and Darkness. It is one of the Pokemon that you can become in the beginging. If you don't get Piplup, it can be found in Crevice Cave(floors 1-10.)
In any floor i found it on floor 2
You can get keys after you beat the game. They are mostly found in Solar Cave, or bought from the Kecleon Market.
Waterfall cave is unlocked when you progress through the main story. I forgot exactly when becuase I found it a long time ago. Sorry. This is all I remember.
I have found keys in these dungeons: Buried relic, Solar cave, Desert resort ( I haven't found any there but i have heard you can find them there.