I have been following these instructions for resetting root password for local installation of
"C:\Program Files\MySQL\MySQL Server 5.6\bin\mysqld" --defaults-file="C:\ProgramData\MySQL\MySQL Server 5.6\my.ini" --init-file=C:\\MySQL-misc\\mysql-init.txt
2014-02-08 15:44:10 0 [Warning] TIMESTAMP with implicit DEFAULT value
is deprecated. Please use --explicit_defaults_for_timestamp server
option (see documentation for more details).
The issue has been resolved.
As stated in my question I followed instructions from MySQL manual.
The process did not go exactly as described (and this was the reason for my original post) but it worked nevertheless (see UPDATE section in my post).