score:4
No. Since the final destination is not a third country, this does not even begin to fulfil the TVOW requirements presented in the question. You must enter and exit the region directly and not transit anywhere else in Russia.
Also, generally when you have a stopover in the same country as your final destination, immigration formalities are processed on the first port, not at the end. There is a high chance that same is the case with this itinerary. Immigration will be processed in Moscow, and Moscow to Kaliningrad will be a domestic flight.
Thanks @Michael Hampton for the following:
The official web site states: "Виза разрешает туристу находиться исключительно в Калининграде и области. Въезд по ним на остальную территорию Российской Федерации с целью транзитного проезда в Калининградскую область или выезда из нее, в том числе через аэропорты в беспересадочном режиме, невозможен." Translated: "The visa allows the tourist to be exclusively in Kaliningrad and the oblast. It is not possible to enter on the e-visa to the rest of the Russian Federation territory for the purpose of transit to or from Kaliningrad Oblast."