The article you linked is quite old, the latest version of Advanced Installer has now built-in support for removing folders like the one you have (i.e. not created by the installation, but by the app). Take a look at the following article, on folder removal operations.
EDIT:
No, you can configure it to not create the folder. As in this sample project, folder test. To do that you first create the folder, then configure the removal operation and hit OK. Then right click on the folder and select Properties, and from the first tab untick the option "Create folder on target machine".
The info about the removal operation will not be removed from our website and it is also a part of the offline user guide from Advanced Installer, so how ever is using version 12.1 will still have it.
We remove from the website only articles for features that no longer exist, and in that case it is useless for me to include detailed steps here if the GUI from Advanced Installer will be different, or the feature completely removed (which I doubt it will be the case with this one).