The .pk3/.log files aren't being placed in the same folder as the .exe file; they are being placed in C:\Users\<windows account>\AppData\Local\VirtualStore\Program Files (x86)\<folder name for wadsmoosh files> along with a folder named pk3.
I ran it multiple times and triple checked the root folder with the .exe; the only reason I was even able to find the .pk3 at all was because I ended up performing a search on the entire C: drive for it.
Is there any way to fix this, because it's particularly annoying?