Mysql – Scheduling MySQL Workbench to execute and export on a daily basis

This is an arguable opinion, from limited personal experience.

I believe it was the Workbench who screwed up the process of round trip engineering several times. I don't remember all the detail, but it certainly synchronized more objects than had actually changed. It silently deleted some data a few times. And it sometimes generated SQL that the server rejected. It was a development DB, no big deal, especially compared to the benefits. But in production I'd rather refrain from being at such a tool's mercy.

Some other people's experience was similar, e.g., MySQL Workbench model/source synchronize issue

So for a production DB there may be risks, including that of losing your data. I would stick with phpmyadmin and do synchronization back into the model, always checking what the Workbench is going to do. Keeping the model just for reference.

The options file in MySQL is a human-readable text file, typically called my.cnf on Unix and my.ini on Windows. This single file contains configuration entries for all things MySQL, including the server, and the client library, and the various other official client utilities.

The screen you're referring to is a glorified configuration file editor for that file.

Within the file there are "groups" with headers in brackets, that determine which portions of the file are read by the different components of MySQL -- the command line client hast its [mysql] section, the various client utilities (like mysqlcheck) will also read what's in [client], and the server itself is configured under [mysqld]. Some of the other utilities may also have their own optional sections, for utility-specific features and options that would not be valid for all client utilities, like [mysqldump].

What they're doing here is letting you edit different sections of a single file, without actually telling you what they're letting you do.

Take a look at your local options file, and this part of Workbench will perhaps be a little more intuitive.