That really shouldn't happen - many creators run their content through the Compressorizer before releasing it and some state it on the download page.
However, I always back up any file before I run it through the Compressorizer - test in game, and if it's fine, then I remove the back-up. I do this before I use any tool, however, because backing up your content is always the safe way to go.
Anyway, the tool has two functions, decrapify and compressorizing. If you are wary of using it for compressorizing, the "decrapify" option does exactly the same thing that the other method (dragging the file over the icon) does because you are using the same tools Pescado provided.
All it is is a container for the scripts. But, both methods work! Whatever is personally easier is what you should do.