This image visually explains the two terms quite well. As you can see, if your mechanical axis naturally goes through the middle of your knee before lengthening, lengthening along the anatomical axis will shift the mechanical axis toward the outside of your knee at approximately 1 mm per 1 cm lengthened. Since force would now be applied unevenly across your knee there is increased concern for arthritis over time.
Keep in mind that one's mechanical axis may not naturally go through the center of the knee. It would be more concerning if it went through the outside part of the knee initially as lengthening would push it outward even farther. In contrast, if it deviated 3 mm toward the inside of the knee initially, lengthening 6 cm would thus make it deviate 3 mm to the outside of the knee and not raise any concern.
All of the doctors I've seen who use G-nail and precice nails lengthen along the anatomical axis. These are some of the best doctors in the world, and it doesn't seem like they think creating mechanical axis deviation of 1 mm per 1 cm of lengthening would cause any significant problems for people with normal legs to begin with. It looks like doctors who use fitbone may lengthen along either axis.