Actually, answer is no. Destination folder for report is saved for list but not for copy/move. The better you can do for now is to create a shortcut in the startup folder as this :
"C:\Program Files (x86)\XL-Toolkit\XL-FileTools\XL-FileTools.exe" "C:\Tests" <-- Input as parameter
Put this shortcut in the startup folder.
If the folders you want to process are on the same volume and options are the same, you can process them all with only one process. All you have to do is use the parent folder, or the drive letter, and copy the list of path as file filters (in contains tab). Ex. :
C:\folder1 C:\folder2 c:\folder3 Etc.
You can save this for a later use.
I don't plan to support all options and function as a command line, but I can add the possibility to save the destination folder for copy/move and most of options. The program will start and all you will only have to select the saved filters, select the copy/mode tab and click on Process button. Will it be useful for you ?