In regards to time travel:
I think it has a simple but maybe not logical explanation; Young Xenahort was told that no matter what he did in the past, it was not going to change the future. So if we look at it from the relative point of our Heroes, nothing has changed for them besides Ansem(the bad) being alive (this being due to Ansem being removed from the past and brought to the present).
Kind of like when Trunks traveled back to his timeline only to find that nothing had changed and that he would have to defeat android 17 and 18 himself.
BOOM GOES THE NERDAMITE!
