"200 course point max. exceeded, final 79 points will not be shown".

you answered the question 

200 course points : coordinates where you get directions

1000 waypoints : coordinates that make up your track

beyond 200 : you will get no directions

someone else to chime in

This sounds a bit limiting for a watch marketed as being top of the range for trail running.....

Will I still be able to see the route on the map screen beyond 200 points???

yes 

Actually, when you send a course from GC to the watch, it includes a coursepoint for every turn. Something really unnecessary. So, if you put your own coursepoints on the course (aid stations, water etc) it's probably that they will not appear after 200 "turns" . Eventually, when you navigate a course, in the Next waypoint field, you will see the next turn. There is a little trick to avoid this. After you place your coursepoints on the course, download the course file as a .fit file on your PC. Connect your watch to your PC and place this file into the Newfiles folder. You will have the course with your own coursepoints but without the turn by turn coursepoints. 

If you don't want to place personal coursepoints just send the course to the watch by sync. After 200 turn coursepoints you will not have turn notifications but the navigation will work correctly. There is also a setting for turning off the turn by turn alert. So don't be afraid of the 200 coursepoint limit.   

When I look at the gpx file in garmin connect. It does not show any "course points". So this is automatically generated by GC when transferring. Correct??

Is this only an issue due to the length of the route (85km)???

Yes, when you are using GC to create the route, course points for turn-by-turn always are auto generated. If there are more than what the watch can handle, the exceeding ones are not showing up. In my 5x I have 50 as max and after that I get an end flag and distance to end instead of next turn symbol and distance to that.

If you want more control of tbt, then you can use another site/tool to create the route. I use plotaroute.com.

There are no course points in GPX files. They only exist in FIT and TCX files (TCX files are text).

Track points (not waypoints) make up the track.

Waypoints are locations that you can navigate to.

support.garmin.com/.../

I tried to copy the .FIT file as you mentioned into the Newfiles folder. It appear to be stored, but then the course does not appear under "courses" when I try to find it. When I reconnect the watch to the PC the file is no longer in the Newfiles folder, and also does not appear in the "courses" folder.