Keep in mind that the nuclear strike that the Soviets launched had a lot of holes in it - there were a lot of facilities that were never touched, a lot of targets left off the list - in other words it dovetails with a limited war as the creators of the game stated
This wasn't an all out strike hitting every target there was - if that was true then places like Niagara Falls and Hoover Dam would have been gone for sure just to take out the huge hydro facilities there, let alone the big list of army and navy bases that were never hit
As for what Soviet commander would leave the port possibly intact? Keep in mind what we know from Last Submarine as to an oversight - that's a pretty big base for subs and it was left intact
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