"Over there" stands for the USSR. "Darkness at Noon" is kind of a roman a clef (a novel that portrays true-life characters or events behind assumed names). Thus, "No. 1" is Stalin, the Soviet dictator who took the Party away from the original ideals of Bolshevism into his own totalitarian vision. As Koestler points out, under No. 1, agreeing with the Party leader is more important than the principles of the Party, or even the truth (e.g. the episode with the submarines).
"Over there" was used to suggest that communist movements in the other countries, still closely aligned with labor, are physically and conceptually remote from the totalitarianism of No. 1's Party (Stalinism). This is obvious when Rubashov has to "straighten out" the dockworkers who still oppose shipping materials to an oppressor nation. In terms of Communist ideals this is a correct position. But No. 1 has other concerns, so the dockworkers have to do a 180-degree turn and allow the ships to pass. For No. 1 the survival of his own regime is more important than the ideals of Communism.
Communism as practiced "Over there" bears little similarity to the workers' version. Nascent "communist" movements which arise locally are closer to the original Communist idea than the Party "Over there," which espouses no tenets and stands for nothing besides the will of No. 1. What No. 1 says is right, anything else is wrong.