Can I use my master's degree thesis (a pilot study not published) as a Research Project Proposal for a PhD application?
If you are asking whether you can repeat your MS work to get a doctorate, then the answer is no. If you are asking whether you can work to resolve still-open research questions that you already worked on earlier then the answer is a qualified yes.
But it depends on where you are and also on your advisor. In the US, for example, you don't normally need to make such a proposal to apply for doctoral study. Other places you do, and in those places the advisor will need to ok the proposal.
It's acceptance also depends on whether the advisor would consider the proposal to have sufficient depth to be suitable as a doctoral research project. So, again, if you are looking for an easy way through the doctorate, the answer would be a likely no.
But in the right place, with the right advisor, and the right problem, it can all come together for a yes, and your prior work might be considered a plus.