"1.) I added a program with Synaptic. 50 packages were downloaded and installed.
2.) In Synaptic I marked it for "complete removal", then executed. Result? 1 package was removed
3.) I opened up console and entered apt autoremove. Result? 14 packages were removed.
4.) 35 packages were not removed."
For larger applications, it might make sense to just download all packages instead of installing them ("download package files only" checkbox in synaptic), then extract them all, and then merge the extracted folders into one and create a .sfs from it.
You can then load or unload it as another layer at any time without installation.
Although, doing this with 50 packages ....