Neither.
Windows is more of my expertise than security is so I'm gonna chime in.
I recommend install Windows 10 Anniversary via bootable usb. This is a new OS and not just a simple update, kinda like 8.0 to 8.1 if you will.
Rufus is probably the best tool because it will allow you to set up the GPT partitions correctly and delete all olds partitions and create new ones. I had a 20GB partition on my HDD from Windows 7 I didn't even know about until this install. (Bought the laptop used) Also it makes things easy as it will install with secure boot enabled with UEFI enabled so the only thing you have to do is enable boot to usb in bios and that only takes a few seconds to do anyway.
I used Media Creation Tool only to download the ISO, that's it. Using windows built in feature or Media Creation for install doesn't delete or format the old partitions. Only when I used Rufus was I allowed to format and delete the old partitions.
Going this route is the way to do a true clean fresh install. No extra time needed and I freed up that HD space I wanted. Most importantly my reboot, shutdown times are amazing. I haven't timed my start times but they are all within 6-10 seconds now vs my long restart times in the past.
Here is the tutorial in case you need help. This tool has been around for years and its trusted. I tried GPT and MBR and both work but GPT is pretty much the better option and error free even on a 3 year old laptop with a 2 year old BIOS
USB Flash Drive - Create to Install Windows 10