Sorry to resurrect an old thread but I own both of these boards and wanted to share my thoughts...
First to answer your question, yes you can mute any part of the style or change instruments in the Korg, just as you can on the Yamaha. You can even make your changes persistent, all of the factory styles can be modified (just reload from disk if you mess them up.) The floppy drive is very slow but gets the job done. Get the PA60 with HD if you can.
The Korg has a better key feel, more sophisticated effects editing, and a better sequencer (allows you to insert and delete whole measures, etc.). It's styles seem more musically complex, modern, and "live" sounding to my unsophisticated ears. Sometimes I have to mute tracks because it seems like there is just too much going on. But if you are playing in real time, you have to time your chord changes just right or it sounds like there is an interruption in the style.
I prefer organ sounds, and I'm dissatisfied with the Korg's panel voices. Not enough good choices for the lower (LH) voice. The Pa50 lacks drawbars or "organ flutes". The Yamaha does a better job approximating real instruments, especially the Pipe Organ. When playing chords with the accompaniment stopped, the Korg Pa50/60/80 do not sound the root bass, so chords do not have the same depth and impact as they do on the Pa1X and all Yamahas going back to the Electone organs of the 1970s.
With programming, there's very little the Korg can't do, but the operating system is much less user friendly compared to Yamaha. Part of the problem is the display, which although large gives limited information on each page. With all of the abbreviations, menus, control combinations, etc. there is a steep learning curve.
The Yamaha has better sounding voices, a wide variety of more forgiving styles (if not as musically complex), and a much more friendly operating system. There is more 3rd party online support, USB ports for computer connection and almost unlimited storage, and a color screen that can even advance the musical score as you play.
The sequencer is probably adequate for most needs. But due to a half-baked implementation of step editing, you can't insert measures or edit chord progressions in a recording made in real time. If you want to do heavy-duty editing, you would be better off using your PC and the XG Works software, which Yamaha unwisely discontinued last year. (Commercial sequencing software does not recognize the Yamaha specific XF meta-events such as chord changes.)
The PSR-3K lacks a panel control for "ensemble" (RH harmony). You can set it up in advance as a preset or assign to a pedal but that's not always convenient. Compared to the punchy bass of the Korg, the Yamaha sounds kind of flat out of the box. Adjusting the graphic equalizer improved the loudness a lot, made it almost as good.
The Pa50 is a great value for the money, and probably better than the similarly priced PSR-1500. But especially now that I have a copy of XG Works, if I had to live with only one board I would probably keep the Yamaha. This is based mostly on the quality of its panel voices, and highly approachable interface. If I had another $2000 to burn (and I could audition one first) I would also consider the Pa1X/Pro.
My $.02,
Ted Sowirka
[This message has been edited by TedS (edited 06-25-2006).]