Thank you Catalin. I'm 'learning as I go' with MSIX builds.
I have a path to a solution for this problem:
I need to package my MSIX file structure in a way that allows the Runtime to be 32-bit and the *.exe application to be 64-bit. I was forcing the Runtime to run inside the MSIX container and not get access to any of the 32-bit dlls that it needs. The *.exe looks at the HKLM registry to find the Runtime installation (in my case inside the MSIX).
Will keep trying some different file configurations but this seems to be my main challenge. I want to package as x64 when it is finished.
Are there any examples of this type of packaging? Should I build -86.msix or -64.msix package?