A high powered pickup will overload the circuit making it distort but that is not the same as distortion from gain. Try it out, use an EMG and a mid powered passive pickup through the same rig with the same settings and the EMG will distort less than the mid powered passive, then play clean and (depending on your amp) the EMG will distort the clean channel from overloading it whereas the other won't.
I have 4 guitars here, each with different level output passive pickups. More winds, hotter pickup, more compression = hits the front end of your amp harder causing more compression in the amp and more saturation in the gain. Period.
EMGs work like they do because they have a built-in preamp and compress the crap out of the tone. That tightness, or seemly clearer gain, you hear using them is why they have a strong love/hate following. I hate the things, but they don't lower the gain.
High gain pickups do not lower the gain coming out of your amp. Most, if not all, high gain tube amps use a cascading gain stage system, where one stage overdrives the next. If you increase the gain and distortion going into the amp you will compress and overdrive the input stage, there-by increasing the compression and gain throughout the whole circuit..
Originally Posted by Dimarzio FAQ
What is a distortion pickup?
All magnetic pickups produce a clean signal with no distortion. Distortion is produced either in the amplifier or in effects pedals or rack effects. When a pickup is said to produce distortion, it indicates a pickup with high output, which more easily drives amplifiers into distortion. An amplifier with a totally clean channel or clean setting may not distort at all, even with a high output pickup.
Too much distortion?
It's also true that using a high-output or "distortion" pickup with the lead channel of a very high-gain amp may create an extremely distorted sound, to the point where individual notes have reduced definition and chords blur together. The best way to reduce the amount of distortion in this situation is by lowering your amp's preamp volume or first gain control.
Originally Posted by Seymour Duncan's FAQ
What is the difference between low, medium and high output pickups?
There are a couple of differences. Low output pickups drive the front end of your amp less and tend to produce a more bluesy or more vintage distortion. They have a very open feel to their tone. High output pickups drive your amp harder and can sound more compressed with a tighter feel. Also, higher output pickups with the same magnet type tend to sound darker because the resonant frequency of a larger coil is lower than that of a smaller coil. Medium output pick ups tend to fall somewhere in between depending on their magnet and wire type.
If what you say is true, that running a hotter signal into the amp lowers gain, running a boost pedal like a TS9 in front of an overdriven amp would get you less gain/distortion. That is 100% false(tube, digital, or solidstate).
Now some people prefer the tone of a high gain amp with a mid or low output pickup. That's a preference and tonal thing, not a gain issue. Others prefer the tone of a high output pickup, or boost pedal, slamming a lower gain amp, or one with the gain rolled back. Using a SuperD, X2N, or Evolution is not going to lower the gain in any amp I've ever played through.