Your are assuming you are supposed to install "inside" the simulator, but that's now how our sceneries are supposed to be installed.
According to official LM recommendations, an add-on should be installed OUTSIDE the simulator, and enabled into it by means of an add-on.xml file. Lots of developers don't follow this rule, so the install "inside the sim", but we do, so we correctly install in our own folder, and properly use the add-on.xml to have the simulator see the scenery.
So, as long you are using an installer that supports P3D V5 ( and all our current installers surely do ), the scenery will surely be enabled in the sim at the end of the installation.