any mats in your startup file will be saved so long as you mark it as a fake user  (click the F next to name )

could open "that" blend [untick load ui if you have blender set up just how you like it , bottom left on open menu]

set the mats as fake {delete the stuff you don't want } then save startup file

or append the mats into your blend then  set the mats as fake then save startup file

hope that helps