When a question is marked as a duplicate, it doesn't necessarily mean that the exact question asked is the same. (The text of the duplicate notice is misleading in this respect.) Rather, it means that members of the community believe that some or all of the answers to the marked duplicate directly address this question, and there is nothing useful to say other than what's already in the answers to the other question (or could be added as an answer to the other question).
Or, to quote another meta post here,
I think it is important to consider closing as duplicate as "these are very similar questions, to the extend that the answers will be pretty much the same", and not "these are absolutely identical questions".
So, a question being different from "duplicate" isn't necessarily a good reason not to close it as a duplicate, if the answers will be the same.
What to do if you disagree that "the answers will be pretty much the same"? Easy: edit the post to highlight the difference, and explain why you believe that this difference could potentially lead to different answers. Then cast a reopen vote, if you have the privilege. (Even if you don't, your edits will push the question into a reopen queue where others can cast votes.)
For example, if the post was previously "Publishing: quality vs. quantity", in the body of the post, note what the marked duplicate says and why you believe the considerations are different when not asked in the context of a single project. Then it will go through the reopen queue where, if community members actually think the answers will be different, they will vote to reopen.
The benefits of this approach are:
- if the answers to the marked duplicate do answer the OP's question, they get (multiple, very good) answers very quickly.
- if the answers to the marked duplicate don't answer the OP's question, then by focusing the question on the different aspect, the OP gets advice targeted to the differences in their situation, rather than just having the answers to the other question repeated (which would of course be pointless).