So, with regards to GeoIP, the plugin automatically makes a geopoint recognized field called location. The add_field lines:
add_field => [ "[geoip][coordinates]", "%{[geoip][longitude]}" ]
add_field => [ "[geoip][coordinates]", "%{[geoip][latitude]}" ]
...are effectively creating a redundant coordinates field. Chances are good that you have Kibana dashboards which are using coordinates, so you should work to preserve that standard, or slowly switch to using location. To convert/rename the existing location field to a coordinates field, you would use:
mutate {
rename => { "[geoip][location]" => "[geoip][coordinates]" }
}