Currently it seems that proposals and reports receive the same title as the project. This leads to 3 DOIs (proposal, report, and project) with the same title.
One option would be to automatically (pre/a)ppend the category. For example, see how F1000 appends version info to titles [1, 2]. Perhaps something similar, but for titles, could be done for Thinklab?
Update: It looks like F1000Research doesn't include their version stamps in DOI metadata, but does so on their website. For example :
iCTNet2: integrating heterogeneous biological interactions to understand complex traits [version 2; referees: 2 approved].
For example, our project  is titled "Repurposing drugs on a hetnet" and hence so is the proposal . You could imagine:
And if versioned citation gets enabled for reports and proposals, which I think is an important feature, you could have:
We've appended [idea], [proposal], [report], or [project] as you suggested.