Unfortunately, annotation importers (such as gff) prompt the user for the sequence to attach the annotations to, so they don't work well under wrapper plugins.
But as it turns out, I was developing a new wrapper plugin the day before you asked this, where I wanted to do exactly that. So I extended our wrapper plugin system to support annotation generators. Unfortunately, the changes won't be available until Geneious 8.1, early next year.
In the meantime, if the command line program has an option to include the sequence data in the gff file (since the gff format optionally allows it to contain sequence data) then you should be able to get it working if you write it as a general wrapper plugin. If not, then the best you'll be able to do is to have it prompting the user to choose the file or document in Geneious that contains the sequence data each time they the plugin finishes.
And no, there isn't a way to see the actual command line. I'll probably include an option to allow that in future versions.
The user selectable options are replace by the [otherOptions] section in the command line template which by default looks like this
-in [inputFileNames] -out output [otherOptions]
If you want the input file name after the other options you could change it to something like this
-out output [otherOptions] -in [inputFileNames]