I can tackle a couple of these at least:

Are there aether points in the body (chakras)? Depends on who you ask. Certainly the Order of Monks (the Fists of Rhalgr) believe so, and this is a big point in the MNK storyline. Those not of the Monk order may be inclined to simply call it how attuned one is with the aether that forms their own life force, but stop short of actually calling it chakra.

Is magic simply aether manipulation? Yeah, pretty much. Not sure what else to say here besides the CNJ storyline says just about exactly that.