Hi @spoonkim,
It's not so much as "always" use a nested family, but more "use parameters to drive size, and not lock to control size, only position". Also nested families are easier to control, also in position.
Imagine creating a Family and have it's height controlled by a instance parameter (with reference planes), if this family is used as a nested family and the bottom and top (refplane) of the family is constrained to refplanes in the host family, you would still encounter this issue when creating a array group.
Instead link a host family parameter to the family to control the height (type or instanced based, depending if the family is shared or not, for shared use instance parameters!)
This could also be used on the extrusion (depending on how it's made), by attaching a parameter to the Extrusion End, see sample below: