Found a solution thanks to the debugging procedure (Method 2) described here https://learn.sparkfun.com/tutorials/ho ... tartup/all
If opening the application with autostart there is no shell window provided as with the IDE's. Running the app in Thonny and IDLE did show that everything was good to go according to my code, but by using the Method 2 procedure that provides a background shell, I could see that the script didn't like that there was no information from the GPS when starting so in some way it has stalled the USB port in a way that didn't pick up the feed when a signal came through. I did experiment with a .sh script and a delay of 10 seconds but apparently that wasn't enough. After changing the code and applying some 'if' exceptions it waits for a proper serial string from the GPS before updating the display.
So now I lean to a conclusion that running the application from Python3 is more error sensitive than using Thonny og IDLE.
In any case thanks so much for supporting me and for all the good and wise advice I have received so far. I hope this case can be helpful for other projects dependent of autostarting in the GUI environment where I can highly recommend 'Method 2' for testing before the application is deployed.