your way to set neutral properties seems to be correct, but be sure, that there is no other property selected in the Properties menu.
If you want to set a paticular property like Color, you will be able only to set this property by using "Set as Neutral Properties"
In this case select the actor/part/assembly, second select the property and than use "Set as Neutral Properties"
But there is no Property to set the Position. In this case you have to deselect all properties and than use "Set as Neutral Properties". This will set ALL PROPERTIES of the actor inclusive the Position.
First image shows the selected Color, second Image without any selected properties!
I've been doing what Dirk has suggested, and I'm still not able to get my part's neutral property to to update just as Blair described. I dont make any changes in assembly selection mode though.
I have no problem with positioning and neutral positions in animation mode, but view mode is not working out the same since I'm not setting keys.