The most common customization in Visio is changing the D-Tools logo to your company logo, which is a completely different set of instructions than this, covered here. Some reasons you might want to create a custom Visio Template are:
C:\ProgramData\D-Tools\SIX\Templates
Example 1: Changing the drawing scale for the schematic page.
Example 2: Adding more pages. Let's say you want to always start your drawings with three schematic pages, one for Audio, one for Video, and one for Control.