This has been discussed so many times on the forum, and it's not a problem or a bug or an issue or something that needs fixing.
It's how the sim works: all sceneries installed using an add-on.xml file, which is the proper and native P3D4-way of installing sceneries, will not be editable in the Scenery Library.
About the error message when installing, it looks like you are installing while the sim is still running or, maybe, too soon after you closed the sim, not allowing enough time for it to close all the running processes.
Installing after a Windows restart should fix this.