It's a great feature that WAB allows to add a GIS URL service as a Search function.
But is there a way that the result of the search is not highlighted with the brownish orange color? Can the result be just simple point? The color coding is a bit misleading. It also would be nice if the pop-up window is not a 'general setting' and it's an individual setting instead.
If you are the administrator of the map service, displayed highlight colours can be configured in the map service publishing stage. In the your layer properties, there should be a property for highlight selection colour.
You can add an on click mapEvent to place a marker at the location of your mouse click.
I am not exactly sure what you mean by: " It also would be nice if the pop-up window is not a 'general setting' and it's an individual setting instead." You can override how each attribute table displays by setting the infoTemplate object the feature layer.