Hello,
I'm glad to hear you have begun your own modernization journey!
In Windows 10, version 1809, we introduced a new type of MSIX package called a modification package. Modification packages are MSIX packages that store customizations - such as registry changes or configurations. That is probably the way to go for what you are describing. You can create a modification package by using the latest version of the MSIX packaging tool (for Windows 10 version 1809 or later). However, those those are distributed - not dynamically generated as you are describing also.
With MSIX there is no restriction preventing you from separately dynamically generating files - so long as you are not saving them to your install directory nor a system protected folder. So if you want to download and/or dynamically generate some configuration file on first run that is an option also, if you wanted to perform that operation outside of your application you might want to check out PSF with the new scripting capabilities - https://docs.microsoft.com/en-us/windows/msix/psf/run-scripts-with-package-support-framework
Modification packages : https://docs.microsoft.com/en-us/windows/msix/modification-packages