Hi Chris!
If I understand you correctly...
Generally you set map extent and clipping in the map frame.
What I do is zoom in or expand to the largest usage area for the map. In your case that would be 1:500,000.
Then center it so your area of interest is in the middle. Create a Bookmark and name it 1:500,000 or something else to your liking.
Then right click the Map Frame, select Properties. Select Clip Layers. Select Clip to a custom extent. Select Current visible extent. Click Apply and OK. Then save your project.
Here's a help page for you.
https://pro.arcgis.com/en/pro-app/latest/help/mapping/properties/clip-layers-in-a-map.htm
If you want to have clip files of your points, lines and polygons, you can create a rectangle clipping polygon, and then do a batch clip and save the 1:250 K clips to the geodatabase. Batch clips are fun to do, too, and serve their purpose if you are obtaining data from cloud server geodatabases, and want speedy load times.
Please let me know if this will get you to your destination.
