Scarcely ___ the station when the train began to move.

'Scarcely' is followed by inversion of the past perfect, and the sequel is introduced with 'when'. So 'had he reached' is correct. Without inversion the pattern breaks, and the simple past 'did he reach' misses the earlier-action sense. After negative or restrictive openers such as not only, hardly, scarcely and rarely, the auxiliary comes before the subject.