I think you are still unclear about the dependencies issue because your first rule is a situation that would most likely never happen. Let's say one wants to uninstall gtk1 and it is in the optional directory and you manually installed it first then XMMS. XMMS installed and the .tce is still in the main tce directory. So according to the first rule mentioned XMMS would not be able to have it's .tce deleted since it resides in the main tce directory. But now you go to reboot and XMMS is broken by a missing gtk1 since the XMMS tce is still in the main tce directory. Mainly, the optional directory is for end use apps that you sometimes use, not libs the system is built with.
Or let's take the reverse and more likely scenario. You have gtk1 installed and in the main tce directory. XMMS is installed and left in optional. You go to uninstall XMMS and gtk1 is not part of that picture as it is a dependency, and not a dependent app. I think dependency vs dependent app is where there is still some confusion. Uninstall gtk1 when you also have XMMS installed and you will get a dialog telling you that XMMS is dependent on it. Uninstall XMMS and you will get no such offer to uninstall gtk1.
In other words, the first rule you mentioned would leave you rebooting into a broken system if you uninstalled the lib or app not installed from the tce directory that has dependent apps with their tce's in the main tce directory. If we are going to offer to delete .tce's at all, dependent apps must get deleted from the tce directory if one makes the decision to delete the .tce's or a broken system upon reboot will result. I must assume that one is not installing low level libraries outside of the tce directory and then placing apps that need that lib into the tce directory. But even in that case, if one chooses to delete the .tce's of both the uninstalled app and it's dependent apps if they are being uninstalled then those dependent apps would need to be deleted from the tce directory even if the main uninstalled app/lib was not in there or a broken system upon reboot will occur.
And avoiding a broken system is the goal in the first place.