The problem is you can't have the USSR fighting the Axis by itself and without LL/significant aid from the UK and expect the later Soviet offensives to happen. Just one example, with the Luftwaffe not having to direct a huge number of assets "elsewhere" and also not losing experienced pilots and other aircrew Soviet forces are going to be exposed as all get out on all those flat open places. Stukas and other aircraft will have a field day train busting, and in the USSR if you mess up rail traffic you hose logistics big time. The USA sent a lot of locomotives and rolling stock, as well as rails to the USSR under LL - if they don't get it it means that every day they have to decide "do we build tanks or locomotives?" (locomotive works in all countries involved got involved in building tanks or at least major tank components). If the Germans and Finns take Leningrad the Axis logistics get better, and any chance the Soviets have of getting supplies via Murmansk go away due to rail interdiction. If Moscow goes, rail transport is seriously disrupted which has some major issues not only in moving troops around but also moving factories around.
Both Moscow and Leningrad were centers of manufacturing. Leningrad did have production to some extent even during the siege, and picked up afterwards. The Moscow factories remained in service throughout the war, in this scenario there will be more disruption at a minimum. All sorts of raw materials from leather to aluminum came from LL as well as finished goods. Trucks, jeeps, radios were all vital for Soviet counteroffensives. As far as Stalingrad goes, if some of the resources that will be available (25+ divisions and more stuff) ITTL are used to shore up the flanks, even if the Germans go in to the meatgrinder as opposed to simply encircling it, things go differently.
Jokes about cannibalism aside, malnourished workers are not producing efficiently and make more mistakes, no matter how the NKVD makes threats (look at the "efficiency" of the slave labor factories in Germany and elsewhere). Malnourished soldiers simply don't have stamina and get ground down quickly, if they are missing vitamins you can see things like night vision going to pot pretty quickly (not a good thing). Whatever LL did, whatever argument you make about "the Soviets could have made that stuff", one of the things they absolutely positively could not make was more food. Also, AVGAS.
Simply saying once this or that Soviet offensive dropped in from OTL happens the Germans are screwed won't work. Even if we assume ITTL that EVERY factory either moved east, or continuing to work in place in spots the Germans never overran OTL like Moscow produces just as efficiently as OTL the Soviets are going to come up very short in many key areas. You have to explain how the Soviets are going to make up for food, AVGAS, leather, aluminum, trucks, jeeps, radios that they got from LL that they did not have or could not produce. The production facilities they had were running full steam OTL, so no matter if all workers were Stakhanovites the only way they have "more" is more factories which they don't have or foreign aid, which they won't have. Oh, forgot MACHINE TOOLS!!!