You should be fine. I use a GK-3 and GK-2 on several baritone length guitars which are tuned to D (so they are NOT tuned as low as standard baritones). I've been doing this for many years, using the VG-8, VG-88 and now VG-99. Not a problem at all.
Now, you WILL get slightly different tone out of the guitar models than you would if you set the scale length to exactly the same length as your guitar actually is. The difference in tone/timber is very much like it is when you set the distance from the bridge to the GK pickup incorrectly - you just get a slightly "off" sound. But what IS "off" and what is "perfect"? To me the question is entirely moot: Does it function and Does it sound good are the two questions I ask.
Now, you WILL get into trouble if you try to tune your instrument below about 3 half steps below standard guitar tuning. At that point you will start to get pitch detection glitches. I would LOVE to tune my baritone guitars down to B, but I don't because my VG-99 doesn't deal well with that. The GR-55, of course, has a Bass mode which you could utilize.
Don't worry too much if the strings that you are putting the GK-3 under are tuned like a standard guitar.