Yes, the OOB setup definitely favors the Axis. By exactly how much and whether the bias requires an Allied bid or merely permits one is an interesting topic of debate. My personal opinion is that given equally skilled teams, 10 IPCs for an expert Allied player or 14 IPCs for a new Allied player balances the game quite nicely.
I’ve never bothered with the fighter intercept rules – strategic bombing doesn’t need to be any weaker, because your average profit on a bombing run is only (5/6) * (3.5 IPCs) - (1/6) * (12 IPCs) = 0.916 IPCs per bomber per turn, which is pretty lousy to begin with. Unlike 1940 Global, strat bombers don’t roll 1d6 + 2 damage; they only roll 1d6 damage. Often the factory you’re bombing will have an inconvenient number of build slots remaining, further reducing the payoff. For example, Moscow can sustain up to 16 damage…which means that if you only send 3 bombers, you’ll average about 9 damage; Moscow can pay $3 to clean up 3 damage, put 2 units in Moscow, and then put 4 units in the Caucasus and 2 units in Karelia. So you send 3 bombers and cost Russia $3, even if none of your bombers get hit by AAA. Yawn. If you send 4 bombers instead, then you have a 33% chance of rolling more than 16 damage, which means you’re wasting between 1 and 8 points of damage per turn. So in practice I’d say the profit on bombing is closer to 0.5 IPCs per bomber per turn.
On maps where it’s harder to cross the ocean, strategic bombing can be a way of projecting pressure. America can get away with strategic bombing Germany in a Kill Germany First opening in 1942.2, because it saves on the cost of transports. But Japan can start hitting core Russian territories (Kazakh, Novosibirsk, etc.) with land units – and win – as early as turn 3, and Japanese bombers can’t reach Russian factories until turn 2, so you’re really not saving much time.