This file doesn't change the defaults for new maps, it only allow the add city layers command to operate properly and add the layer to an existing map.

To change defaults for new maps, the only way is to edit the template they are based upon, but there is no global file to edit to apply to all new city maps, you need to edit the templates for each style individually.

Yea, this is one of the cases where you have to use Edge Fade and not Edge Fade, Inner. One of the differences between these effects is that edge processes each differently solid colored polygon individually, while edge fade, inner processes the entire combined shape on the sheet.

To use Edge Fade, Inner here, the borders would have to be on individual sheets where the number of sheets equal the N-color problem for your layout.

The installer contains updates not just to the main program, but also to the add-ons. so even if you have the latest program version, there will still be things in the updater that updates the add-ons. This is why it should be run at the end after installing everything.

What do you mean when you say things are gone though? Is it replaced by red X'es, or just completely gone? If it is the former, it means that you are missing art resources you used to have installed, which probably means you forgot to install something on your new install.

And here's @Maidhc O Casain's entry added to the atlas:

Probably just the arrow head being tiny. Use Tools -> Set Properties -> Arrow Style and change it to something more reasonable for your map size.