What was the service ceiling of the best Soviet fighters? As I recall the Zero had to really stretch to get high enough to attack a B-29.
No Soviet fighter was capable of intercepting the B-29 until jets. The post-war La-11 was actually deployed in Korea to hunt B-29s and found they simply couldn't do it, and actual wartime models with greatly inferior performance sure as hell can't.
The issue isn't ceiling. A B-29 with full bomb load only has a service ceiling of around 30k feet (note that's defining service ceiling as the altitude where the plane can climb at 100 ft/s, most numbers floating around the internet use much looser definitions), and cruise at 25k and most soviet fighters with 2-stage superchargers (ie only a small percentage, but not because they couldn't make them) could hit that. The issue is critical altitude. The B-29 had absolutely absurdly good turbos, giving it a critical altitude of 31,500 feet at maximum power. With the whole reduced air resistance thing, a B-29B carrying a 10,000 pound Mk III bomb has a combat speed of 360 knots (414 mph!) at 31k feet. Soviet 2-stage superchargers on the other hand, start losing power over 13k feet. In practical terms, the B-29 goes faster the higher it goes, while Soviet fighters are faster the
lower they go. A B-29 at its ceiling is
faster (or not slower in the case of the A variant that kept its turrets and gunners) than any of the Soviet fighters at that altitude and can simply outrun them, or force them into a slow stern chase where they are sitting ducks to the tail gunner.
The USSR didn't have helpless air defense networks like the Japanese. The plane carrying the bomb might get shot down trying to bomb Baku.
As for having regular flying missions with the B-29's that don't drop bombs(like in Japan), well, I don't really think the Russians would turn down downing B-29's flying overhead such an important area.
As mentioned above, that's really not an issue. Not that the USSR
had an air defense network in 1945, they hadn't really needed one when air warfare on the East was more or less entirely tactical, it was all developed post war.
Even if the allies didn't have an army at all, would the soviets have had enough supply trucks to supply an army in France? Seems like during WW2 they were pretty reliant on the allies to help them with logistics.
The answer to that is yes, as long as the Allies don't knock out the VVS quickly and blow up the supply convoys. Sure, the Soviets were dependent on Allied help to build up all their motorized formations, but in 1945,
they are already built up. If war breaks out, the Allies can hardly go to Stalin and ask for all their trucks back.