John has said that he usually prefers lower output pickups because he can turn his amps up louder and get more tone or color out of them that way. So it really means getting more amp tone from them.

John has never really seemed to go for a hot, in your face, harsh type of guitar tone. Higher output pickups like Texas Specials and Lace Sensors have a lot more bite and midrange and aren't really condusive to the sound John likes, especially nowadays.

Here's another example other than John. In my strat I have normal classic strat pickups (its a Mexican 70's Reissue strat). My bandmate has the nicer Buddy Guy strat with the Lace Sensors in it. One time I was playing on my strat and he wanted to trade strats just for kicks. When I plugged his into my amp it was really loud and harsh compared to my strat. So I had to first turn my amp down a little bit and then adjust the EQ settings.

So there is a big tonal difference in higher output pups than lower output. Different players prefer different output. Its all up to your own ear.

When you hear John playing his Relic strat compared to his Monterey Strat or his Reverse Proto strat, the tones are different because of the really low output of the Relic.