I am planning to use metal grease on the wheel bearings (tapered bearings) of my pre-2000y Harley, but I am concerned that it will flow out of the seals and reach the brake rotors because the viscosity is much lower than regular bearing grease.

The recommended use is to apply your LS Bell Hammer series to the outer ring and inner needle of the bearing, and pack more metal grease into the bearing because metal grease is harder to spread to the back side (especially the needle) than regular grease.
Also, if you cover the shield properly, there will be no brake-related problems.