If the difference is a divider resistor, can always stick the FB pin out on a sheet connector and put the reference resistor there.
Annotation works for component values, but won't generate varied net names for power ports unless you use strict hierarchical project settings. Strict hierarchical is usually more annoying than useful because no power ports connect between sheets, you have to connect all of them through sheet ports. If you like to use descriptive net names for power supply sections, for example, this may not be an effective method.
Tim