The difference between clean install from bootable USB flash drive and from the built-in recovery disk
The short answer is that there is no difference to the end result. The difference lies in the process. 

As an example, your current USB installer will install macOS Sierra 10.12.0. After installation you will still need to update it via the Mac App Store to get it back to macOS Sierra 10.12.5. 

If you erase and install from the internet the version installed will already be macOS Sierra 10.12.5.

You can also startup from macOS Recovery and may be able to install macOS Sierra again without the need to re-download it.

But to answer your question, whatever you do makes no difference to the end result. In this case you just have a number of roads all leading to Rome.