Many 3 panel (3 chip) projectors launched in the last 2-3 years that sell upward of $2000 now sport a panel alignment feature. While a few years back some projectors literally shifted the pixel mapping in 1 pixel increments, that mostly has been replaced by digital shifting. In theory, digitally shifting in one pixel increments was a broad sword, not a delicate tool, it worked great for projectors where horizontally one or two of the colors was inherently more than a 1/2 pixel off.
Today though, it's all done in fractions - in this case 1/16 of a pixel, which means we're not really moving the pixels in line (digitally or physically), but rather, using software not too different than keystone correction, to bend one color. It works well enough, better to have, and to use, than not to.
The JVC converged well enough using the adjustment system. It took about 5 minutes to go through the process and recheck the results. If you are fanatical, you can spend more time on it. Best solution? Have a projector that's almost perfectly aligned physically! Still, this system can be very beneficial. Ultimately though, you are sacrificing true pixel mapping, which like implementing keystone correction (but not near as serious), is generally best avoided. I get a headache just trying to think about how panel alignment used in conjunction with Eshift affects the picture at the pixel level.
Bottom Line - Use it. Take your time, it's easy. Then you can compare to the unadjusted by turning it on/off. All considered, the call is yours whether to use it. If the projector is very close to ideal right out of the box, (so you don't notice any color fringing from say half your normal seating distance from the screen), then you may very well prefer not to use this feature. Most will though. It's your call.