Yes, Real Madrid's chances are better and more prepared to face the El Clasico match later than Barcelona.
Los Blancos already have perfect points in the champions league group, it is quite advantageous for Don Carlo's squad to be more concentrated in La Liga.
Unlike Barcelona, they must concentrate on the Champions League match before they travel to the Santiago Bernabeu, Madrid's home ground. meaning, Xavi's attention will be devoted to the champions league match before thinking about the El Classico party.
Barca must win this match over Inter, but if they lose. Barcelona is unlikely to have any chance of qualifying for the next round. Xavi's attention will automatically be devoted to the La Liga trophy.
Due to the fact that there is a team in the group that is more likely not to score a single point, Barcelona, even if it does not reach the playoffs of the Champions League, will fall into the Europa League. Xavi said last year that it would be nice to win the Europa League, so I don't think that after the Champions League group stage Real and Barcelona will be in a different position - both clubs will continue to fight in Euro cups and neither will have extra rest compared to the competitor.