iOS 10 update, info

It is a good plan to use iTunes to back up before doing any updates, and then do the download and install. It is also best to encrypt these backups so it will include passwords and other secure information. I backed up all three iOS devices ahead of time in prep for the update, but did the install over my home WiFi. No known issues. As with all updates some have issues, some not.

The point being...
You only have two options when updating.
If people are reporting less problems doing it one way why not do it that way.
Besides that a backup is always recommended before an upgrade and that is done with iTunes on your PC.

You will get the same update regardless of how you do it. When you do the update through iTunes the device still installs the update. Some of the problems were early on too many people were download the updates at the same time it the servers just could not handle it. Happens the first few days of a major update. So, short answer is that it does not matter how you do it.