Popularity is not a reason to dismiss a reasonably well-established approach to bundling applications, their dependencies, and associated configurations. Docker works decently well in Windows via Docker-machine from what I hear.
You could also put your application in a VM and ship that; there’s plenty of precedent out there, even though it’s not the most efficient approach.
To expand on @tk3369 's suggested approach, there was some discussion about a related question here (permalinking my response because I consider it a solution to this problem as well):