In the Config window, there is an MP3 tab. Within this tab the "Flac Encoder" can be selected, if flac is installed properly. So far so good.
If the Flac Encoder is selected, all the controls in the window do not have any affect, because Flac Encoder does not have the same kind of parameters as MP3. So these controls should be disabled if the Flac Encoder is selected.
The most important parameter for flac would be the compression-level, which is specified with -0 for the worst level and -8 for the best level. May this parameter could be shown in the window insted.
Extra Options in the mp3 tab is functional for the flac encoder. You can use --best to specify the highest compression ratio.