Include
In the certified word there is equipment that is required for the airplane to meet the type certificate. If possible, include provisions that allow changing items. Example, any propeller of xx dia. to xx dia. that turns between xxx and xx static rpm, Any TSO'ed tire of any size, Any O-320 or O-360 Lycoming.
Generally speaking if the aircraft needs it (engine, brakes) it's listed as required equipment. All other installed equipment is listed as optional, and if it is not included in that optional list, an STC or feild approval is required to install it.
I'm not sure what is required in the armature built world and it sounds like from the other poster that your DAR may be requiring something from you that isn't required.
I would really like to see chapter and verse (SFAR's) on this topic.