Collect Files default save folder should be the same folder where the original file is by default.
When you collect files why would you want them in a previously opened, different project? If anything, you want to start in the folder where the original project file is.
Right now After Effects suggest you to collect files into a folder that has NOTHING to do with your currently opened project. How impractical and misleading it is? I've just lost one of my projects assuming I've collected files in the same folder where the original project was.
Maybe add it as an option in Preferences? Default Save location: "local folder where the original working file is".
Seriously, this is one of many workflow flaws of Ae. Please review your whole software architecture and behaviour, listen to your users and try to improve the core functionality in the next version. Surely motion designers will appreciate practical and logical interface more than 3d bells and whistles.