Much depends on how we use those 2-3 weeks to prepare.
I remember the CL final between Milan and Barca back in 1994. Milan had won the league early and were just preparing for the final. Barca had a decisive league game 3 days before the final. Overall, Barca, Cruyff's dream team with Guardiolla at 6, were considered favourites, for they had Romario and Stoichkov in attack and were on a fantastic winning run. But Milan beat them 4:0.
Pep played in that game and knows perfectly well the importance of being fresh in the final.
It was bad for Chelsea that they lost the final yesterday, no two ways about it. The second consecutive loss hit their confidence which may lead to nervousness and mistakes in the next games. They will give everything to compensate for those losses and to finish in top 4. This may lead to more fatigue and some injuries. Fatigue is felt stronger when you lose. Two consecutive losses will "help" them feel in their bones the brutal schedule in April and May. Mental fatigue may creep in as well.
They are good, they have a lot of talented players (calling their players and manager average is incredibly stupid), and it won't be easy to beat them. Unlike the games with Arsenal and Leicester, they will be underdogs and will play with tactics that suits them more. But, ultimately, they are not likely to be as fresh as our players, and this may be decisive.