Installing asset package individually

You must install a flat bundle (which is what you have currently where your .appxbundle does not contain your .appx packages) through the bundle and not through its individual .appx packages. Installing .appx packages (that are part of a bundle) by themselves is an unsupported scenario. This is because the .appxbundle is the package that contains the references to the individual .appx packages and ties them all together as one app. Is there a reason why you want to individually install the main and asset packages?

You can however update individual .appx packages of a flat bundle after the initial install. For example, if your v1 flat bundle is composed of an .appxbundle, x86 .appx, x64 .appx, and an asset .appx, and you know that your v2 bundle only has changes to the asset package, then you only need to build the .appxbundle and the asset .appx to be able to install the update. (You need to build the .appxbundle for v2 also because the bundle keeps track of all the versions of its .appx packages, so by bumping the version of the asset .appx to v2, you need a new .appxbundle that has this new reference. The v2 .appxbundle can contain references to the v1 x86 .appx and x64 .appx; the .appx packages of a bundle does not need to have the same version.)