>>mike_h+(OP)
I mean, from what you said, "the installer" isn't your product, no? The build system is your product. The custom installer that the build tool emits is just something you had to create as a workaround because the Microsoft one sucks, and which is a pure cost center for you, and one redundant to Microsoft's own efforts.
Wouldn't you prefer to have your build system just emitting .msix for Windows, with the expectation that all Windows systems will then run your good installer in response to opening any .msix?