UPDATE 1
I have just tried using a Generic database -> Native (JDBC) connection with the 5.1.49 driver and changing the Custom driver class name to the old 'org.gjt.mm.mysql.Driver'.
Testing this in 9.0, it connects OK (no sha2_caching_password issues) , however, the Table Input still retrieves the columns as 'Field1, Field2' (see screenshot).
To validate that I am using the correct driver, I removed them all and it couldn't load the driver. I also had to change the driver class to match that of 5.1.* so I am 100% certain of the active driver version).
I will keep investigating and update accordingly.