Why is this site-policy but this is scope.
Site-policy is wider than scope, but both are common enough terms that I understand why both are in use. However, I don't think it makes sense to make a distinction between the two in the tags so I support your proposal to synonimyze with site-policy as the wider master.
There is no distinction about:
Changing site policy. 1
Using site policy. 2
And we should fix that by simplifying the tags, not creating more of them.
Given the above two examples, you may say specific-question is the distinction, but it's not included in all questions, and shouldn't be added in others.
If specific-question is the distinction, than that tag, specific-question, is doing it's job. That has little bearing on the rest of the tags used, they have their own jobs, so I don't see a problem with this in regards to synonimizing.
Some questions don't have either site-policy or scope. And so it's not clear what to search for these questions, or what I should tag them as when I do find them.
Tricky. In part this can be determined by looking at the answers, but that has it's own pitfalls. Synonimizing would at least fix part of the problem, since we no longer have to decide which of both it is: pick the master tag.