I think a lot of the muffled aesthetic is a consequence of the decisions made in the recording/mixing process, there's a strong room reverb across the recording particularly noticeable on Ringo's drums which combined with the high-end softening of the Fairchild 660 compressor featured on Beatles records gives it a "rock concert while standing in line for the bathroom" color. I could be mistaken but it sounds like a lot of the instrumental parts were recorded in single takes in the same room compared to say Abbey Road where it sounds like they were tracked independently. A consequence of tracking multiple lines together is there can be cross-instrument fuzzing that results in "muffling", it can be an intentional effect though for a more live sound. Just my 2c