The cheap answer is that if Germany is building a big strategic bomber arm, then it isn't doing something else. Leaving that aside...
A decent German strategic bomber arm still means that most Soviet heavy industry is out of range.
Strategic bombing is expensive in men, machines, and money. Pilots will be used up terror-bombing who would otherwise be supporting the Germans at the front. Fighters and pilots for them will be in shorter supply. Attrition on the strategic bomber forces is heavy: if they are going in under fighter escort then the situation isn't much better for the Germans than OTL, if they're out of escort range losses are high. Russian AA will become fairly high quality as well.
Transportation is less of a problem than you might think. Hitting railways and bridges is difficult in the best of times, and that requires experience and luck. While the Germans are on the advance, blowing the rail links and bridges close to the front isn't all that helpful. By 43*, the Soviets have all those lovely lend-lease trucks supplying the advancing Red Army.
One think you've probably done here is to butterfly the V2 and V1 programs out of existence. With consequent effects on the career of one Wernher von Braun, and the history of space flight...
Refineries? Out of range, most of the time. Except maybe as the Germans near Baku.
Unless strategic bombing is the Nazi hair that breaks the Soviet camel's back at the worst of 1941, it won't do much to not lose the war.
Military: The same, in the overall picture. A tiny bit worse, if you happen to be a Soviet civilian behind Red Army lines, a tiny bit easier if you happen to be a Red Army fighter pilot or soldier. Better, if you happen to live in London in 1943-1945, since the V-blitz goes away. Worse, if you like the OTL US Space program. Better, if you think the US space program was a dumb white elephant. Different, since "if we could put a man on the moon, then we can [unrealistic expectation here"] requires some editing. Also different in modern debates about the morality of strategic bombing.