I've met plenty of Estonians who have a Russian ethnic background, however identify as Estonian, speak Estonian, and do not consider themselves Russian. Again, I think the point of what I was getting at should be clear.
And, to your point about them being called Russian in Estonia, I've heard them called "Russian speaking" more than Russian. Then, again, the Estonians I know take a pro-integration position on the matter. The "ethnic Russian" terminology is often used in pro-separatist circles to justify non-integration, or by anti-Russian Estonians.