Currently I have a .MSI package Ive created using WIX toolset. Ive used a simple command file to execute heat.exe to harvest, candle.exe to get product definition and light.exe to build.
I have a 10 config files I have edited from the original build. Usually I have the customer uninstall and install the new build. However could I build the .MSI updater, using WixTool set that JUST includes the new config files(flat files)? The only requirement from the customer, is the deployment even if its an update must be a .MSI
What you are describing is called a "patch". See:
https://wixtoolset.org/documentation/manual/v3/patching/
https://wixtoolset.org/documentation/manual/v3/patching/wix_patching.html
That won't generate an MSI though. It'll generate an MSP. Perhaps this is understood by the customer.
I have to be honest though, patching is very tricky tricky advanced stuff that takes a deep understanding of Windows Installer, a disciplined release management approach and is easy to get wrong.
How big is your MSI? Is it large enough and being sent to enough clients for all of this to make sense? (Example 1GB game with a patch containing a handful of dll's and texture files going to 1M customers) Or is it perhaps a typical line of business app weighing in at 50MB going to 1 customer. In that case I would just do a standard major upgrade.