Yes, at first it does not make sense, why different behaviour when they are both timeouts, but...
As mentioned, we cannot lock the folder as long as there is an open document in that folder because application is locking the document and the operating system is not allowed to eject the volume on which the "busy" document resides.
So we took our best guess saying that when Mac becomes completely idle, there is a better chance that you finished your work on the document and that it might be closed. Of course there is no guarantee it will be closed, but the chances are higher.
On the other hand, once you unlocked the folders you need and maybe locked those you do not need any more, you will not need the Espionage window for a while, so it makes sense to lock it, just in case somebody manages to gain control of your mac, so that he cannot unlock further protected folders.
In both cases you will probably want the timeouts to be set to relatively short time, because espionage takes care of the rest, in case of Espionage application it will lock the app after this, relatively short time, and in case of folders, it will lock the folder after, again, relatively short time after you stop using your Mac.
You of course might disagree, but I just wanted to describe the idea behind the design.
I hope this helps.