Let me be more specific.
Lubrication-
If you intend to use an oil such as Moebius V106, a general purpose thin film lube, Nikon's recommended procedure will work- at some risk of eventual migration of any excess lubricant to places where it is not desired.
On the other hand if you are using a modern "oil" such as Moebius Synta-Visco-Lube 9010-Film, a fully synthetic lubricant developed in part for use in cameras and optical instruments, the risk of lube migration over many years is truly minimal as the adherence of this product is excellent. Applied as I noted above you're transferring only a small portion of the very thin film remaining on the oiler to just two points on each ball bearing. The result will be substantially less than oil in the mechanism than a single drop spread around the race. The lubricant film, a fraction of a micron thick, is what minimizes wear and friction. Any surplus is wasted.
Magnetism-
As a general rule stray magnetism is not desirable in proximity to low power electronic circuits. What is present after use of a small, relatively weak magnet to control ball bearings in disassembly is likely to be harmless. That said, if I notice relatively strong magnetism is present I use a demagnetizer on the balls.
Bob