In the project Search filter tab, there are four filtering options: “All”, “In Packages”, “In Assets” and “Runtime”. It would be nice if the editor remembered the last setting I used instead of defaulting to “In Assets” every time. An alternative solution that would be almost as good would be a Preferences setting for the default filter.
You could try calling ProjectBrowser.SetSearchViewState using reflection to change the initial filter at project startup.
The Project view is a very old component in Unity and lacks much configuration and extensibility. It’s due for a UI Toolkit rewrite at some point, so I don’t think quality of life changes for the current one have a high enough priority.