This is a good idea. In fact we'll be adding something similar to this in wyBuild 2.7 (coming before the end of the year). You'll be able to build the installer bootstrapper directly from wyBuild. You'll only have to build it once and it will always download and install the latest version of your software from your site.
But for now (as of wyBuild 2.6.x) you can do as you suggested. Build an installer boostrapper with version "1.0" of your software which is just a blank slate: wyUpdate.exe and the client.wyc file. In the wyBuild project for version "1.0" include no files and no registry.
Then when you install using the bootstrapper you can launch wyUpdate.exe which will install from this blank slate "1.0" to whatever the latest version is.
This is a really good idea. It's a clever use of wyBuild and wyUpdate that I hadn't thought of.