As mentioned in a recent thread here, I wonder if this problem can’t be partially solved by the install process looking for main.pd and treating that as the root of the patch?
For example, if the .zip file is not properly formatted and does not contain a subdirectory, then the installation process can detect this by finding main.pd in the root of the archive, and remedy it by creating a new directory to contain the patch. The name of this directory can simple be the .zip file name. This won’t solve the problem when the installation happens by unzipping the patch manually, but it could result in less issues when installing via the Organelle menu. 