Even if we play a "Chelsea team" it still means Guardiola and the coaching staff spending 2-3 days supervising the EL match rather than preparing the team for the next PL game. It still means that the first team players that are not involved are limited in numbers during training, ticking over rather than focusing on the next game.
Given all the problems you note, the huge financial hit and the CL coefficient issue it just goes to show how stupid it was to not go all out for points in games like Southampton, Villa and the like.