I suppose it depends a lot on everyone's personal interpretation, but it makes sense to me. Before Vaatu tore open the spirit portals (likely a more deliberate version of what Korra did at LoK end), you have a human civilisation. These people or at least some of them can use energy-bending. Vaatu invades, spirits take over the world and the civilisation collapses.
The last remaining humans are kept alive by the lion turtles for one reason or another and they give them the ability to manipulate the elements to protect themselves whenever they leave. Given 10000 years pass with these state of affairs, the new culture probably has nothing to do with the old one.
Then Wan happens, and the era of the avatar begins. The lion turtles give them bending which they master by observing animals with natural bending. We've seen both Toph and Wan do this with badger-moles and dragons respectively.
Any lore lost or differences in bending styles can easily be explained away with the sheer amount of time that passes. Even the fire nation forgot the original form of bending as a whole canonically.