I have been facing the following error intermittently.
Authentication to host \'127.0.0.1\' for user \'root\' using method \'mysql_native_password\' failed w
I had the exact same problem performing the upgrade on a windows form application. The solution I found was to change the server, because that one was in trouble. On the server that was presenting the similar situation you described had installed WordPress with MYSQL 5.6.34, on the other I did a clean install with MYSQL version 5.6.26.
I don't know if it has to do with the environment variables used. I believe it has nothing to do with Connection Timeout, if it is a property that is used only with the open connection. This error occurred in a shared environment as well as in a local installation with Maria DB. Another problem I found was that one of the selection commands that retrieved the data was having a problem in its formation not respecting the blanks:
SELECT COLUNA1, COLUNA2 FROM TABLE;
I made the change to SELECT COLUMN1, COLUMN2 FROM TABLE;
I am still testing on this solution I presented, and as of the time of posting there were no more errors.