After testing it, I've confirmed my theory; this application only adds/overwrites files that already exist in the save data directory, while svdt imports all files you selected into the game's save data. This is, again, a minor issue, but an annoyance for some people.
So in order to import all saves, you'd need to create save files for each slot that you are trying to import into, just so the program will overwrite it with the exported ones? Seems like a simple enough fix for the dev to implement.