I have no idea why someone would recommend this. I suspect it is just superstition. There generally isn't anything important or useful to you outside of the DCIM
folder, and you certainly don't get any benefit in copying that folder vs. copying its contents — your computer does the exact same thing either way.
Canon's MISC
folder is explained at What is the function of the MISC folder on my memory card?What is the function of the MISC folder on my memory card? my Fujifilm camera has a similar FFDB
folder. So, even if yours wasn't empty, it's not something you need on import. You can just copy the image and movie files you actually need by whatever method you want.