Apologies, I'm getting a little confused about which machine is running which version of Windows.
As you stated, using the Windows 10 media creation tool on a Windows 10 machine that was upgraded from Windows 7/8.1 could damage temporary files that would prevent a roll-back to either Windows 7/8.1. If you don't intend to revert to either of those, no need to worry.
Licensing works differently depending on how you install Windows 10:
If you're installing from the ISO on a machine that has a formatted HDD, you will need a valid licence key to install. This can be a Windows 7/8/8.1 licence that hasn't yet been used to upgrade to Windows 10 or it can be a new Windows 10 licence purchased from Microsoft.
If you're installing Windows 10 while running Windows 7, for example, using the 'Upgrade now' link on the Windows 10 site, the tool will detect your current Windows 7 licence key and Windows 10 will be activated.
The end result is the same, once the machine has an activated copy of Windows 10, any subsequent re-installations of Windows 10 on that machine will not require the key. Microsoft will detect by a hardware profile that it's the same machine.
Hope that clears it up a little!