The difference between clean install from bootable USB flash drive and from the built-in recovery disk I would like to clean install my MacBook Pro (Early 2015) with macOS Sierra which is also already installed up to the latest 10.12.5 version. 

I Googled how to and found the macaw article How to Run a Clean Install of macOS Sierra. This article covers clean installing with a bootable USB flash drive.

I also found on Apple Support article macOS Sierra: Erase and reinstall macOS as erase and reinstall from the Internet or the built-in recovery disk. I also found the same instruction on Apple Support at How to reinstall macOS. 

I want to do a clean install because of wifi connection issues. I'm currently using internet from an iPad Personal Hotspot. I have difficulty downloading MacOS Sierra on mobile data from Mac App Store or reinstalling from the Internet. Downloading 5GB from a coffee shop is also not convenient. I do have bootable USB flash disk of the original macOS Sierra (when it was first released).

May I know 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.