ApexSQL Doc for MySQL can create documentation in 6 different output formats:
Yes, when the connection to the server is established, select the desired databases from the database list for documentation
Yes, this can be done. When the database is selected for the documentation, go to the Database objects tab, then from Object type grid from the middle of the screen, select desired database objects for the documentation
Yes. From the home tab, click on the Defaults button. Project default options dialog will appear. In that dialog, you can define your own Project default options
No, if you are already connected to the server, the Refresh button can be used to refresh the connection with the server. This button is in the middle of the right side of the main diagram window
Yes. This can be done in the Custom text tab under the Output options panel. In the Image field, click on the browse for folder, select image file path, then click the Open button. (this can be done only in CHM/HTML output formats)
ApexSQL Doc for MySQL can document the following MySQL database objects:
Yes, stored procedures created for replication are included in the documentation