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I would compute the features (ORB, etc.) as usual and then check each keypoint's scale variable and only match those features having the same scale. I think this is the easiest way.
Alternatively, you can do as suggested by @Eduardo and yourself, i.e. compute the scale space yourself, e.g. Gaussian scale space and compute in each level features which are not scale invariant by fixing their octaves (and sublevels) to 1 (and no this is not a "hack", it's just one way to solve it).
