You are experiencing this because even though you change the asset in graphics settings, there's still an asset assigned in Quality Settings being used. The asset in Graphics settings is only used as a fallback when there's no asset assigned in Quality Settings. This is the difference you see in the projects as the 3D template has different quality assets for different quality settings levels and the other project doesn't.
In order to achieve what you are trying to do, you have to change the asset in the current assigned Quality Setting level.
There is plan to rework the UX around setting the render pipeline asset in Graphics Settings. so this workflow becomes less confusing.