The transition table does not necessarily empty the pipeline. Indirect branches are predicted on modern processors, and industry predictors do a better job than you might expect. Obviously, a correctly predicted indirect branch does not cause a breakdown.
Non-branching is generally preferable, but often impossible (or introduces so much overhead to be a net loss). Replacing jump tables using a sequence of conditional branches is sometimes useful, but only if the number of branches in the replacement sequence is sufficiently small.
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