As you overwind a pickup it makes it gives it more output, compression, adds midrange and decreases the treble.
Vintage output pickups are generally more open, articulate (uncompressed), clearer and brighter sounding.
The extra midrange seems to help a high output pickup cut through high gain, but it makes the pickup sound a little too 'middy' when used clean.
The slightly scooped midrange in a vintage output pickup can make it sound a little muddy with high gain, but it gives it a more pleasant sounding clean tone. That said, sometimes a 'muddy' pickup in the neck is a good thing.....it gives killer slur to legatto lead lines and you'll have a better tone as you roll down the guitar's volume.