I know this post hasn't been active in years but please reconsider adding this feature! To avoid increasing the complexity of the GUI, I suggest that when selecting a file under "destination file", that every time you enter a folder, the path to that folder is stored in the textbox for the filename. If you offer a filename, then all the data is concatenated into that output file (current behavior). If you simply omit a filename, then the folder you are in becomes the output folder, and every selected file gets converted and saved in the selected folder with the exact name it already has, except it gets the extension corresponding the the selected file type.
That way, there is absolutely no change to the GUI from a UX standpoint. The dialog I use to select the output destination is exactly the same, EXCEPT that if I don't select give a filename, it treats the last folder entered in the dialog as the destination folder batch-converts all the files. This would be SO USEFUL. I would greatly appreciate the opportunity to use the GUI to do batch conversion, and I strongly believe that it does not need to complicate the interface.
Is there a problem with designing the interaction in this way? I understand that the feature may be a significant undertaking from the dev team, but it would be greatly appreciated! There is clearly a lot of interest in this feature, and I for one would absolutely love to see it implemented. Thank you to the devs for developing such a useful and open-source project!