I've owned and flown 1 or 2 airplanes over the years, and if they had retractable gear I always balanced with the gear up, and aimed to be either right at the middle of the CG range, or in the foward half of the range. I have never experienced a problem with a bird going to an extreme of the range when the gear cycled. This included a large EDF with three rear retracting gear, all with very heavy wheels on them.

And IMHO, you want to balance gear up, because there is always the possibility of a gear up landing, and you don't want to get low and slow gear up and discover you're in the unmanegable part of the CG range...