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No, B-17s do not ever seem to have attacked the Japanese Home Islands. The Chomsky claims are a weird mixture of truth and fantasy.
There certainly were B-17s based in the Philippines in 1941, mostly destroyed by Japanese attacks when the war started. They could not have bombed Japan from there, as they didn't have anything like the necessary range. The B-17's combat radius was less than 1,000 miles and the round trip from the Philippines to Japan is 3,000 miles or more.
If the use of bases in Siberia had been possible, B-17s could have attacked Japan, but this would have involved the USSR going to war with Japan, and Stalin refused to do that until after the defeat of Germany.
While B-17s served as bombers in the Pacific until mid-1943, they were never based anywhere that would have enabled them to reach Japan. After that, they had been replaced by B-24s and B-29s. B-17s were used as lifeboat-dropping aircraft for air-sea rescue for the rest of the war, and for years afterwards, but that isn't bombing service.
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B-17's wouldn't/couldn't be used to bomb mainland Japan until just before Operation Olympic. They, along with B-24's and Lancaster's could use fields in Okinawa an a couple of Islands scheduled for invasion at the end of August, beginning of September, just south of Kyushu. It would have taken that long to build up the fields and move the Air Groups from Europe to Okinawa. At the same time, most B-17 units were transitioning to the B-29 anyway, so mostly B-24's would make it, but not B-17's.
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True, true. There were but two bomber groups in the South Pacific Theater that operated B-17s, the 19th and the 43rd. The 19th had been in action since the beginning and with arrival of the B-24 equipped 90th Bomber Group, was rotated back to it States. The B-24 proved superior to the B-17 due to its designed long distance over water capability. The in-theater 43rd Bomber Group transitioned to the B-24 by mid-1943, and USAAF B-17s in the Hawaiian Sea Frontier command were replaced By B-24s shortly after Midway as well, and that was the end of B-17 deployments in the Pacific. No, B-17s did not operate over the Japanese home islands at any point in the war. For the bare-bones presentation on the B-24 supplanting the B-17 in the Pacific and CBI theaters see https://warfarehistorynetwork.com/2017/06/30/boeing-b-17-flying-fortress-vs-the-consolidated-b-24-liberator/ In addition to the long-range reconnaissance missions for the USAAF, the USMC and the USN operated the PB4Y, the naval version of the B-24, in long range patrol and photo-reconnaissance missions.
Late edit, now that I think a bit more, Add that the only B-17s flying over Japan during the war were being flown by the Japanese. They had three of them, one pieced together from pieces-parts from wrecks in the Philippines and two captured intact in Java.
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Since other answers pretty much explained that B-17 was not used against mainland Japan in actual war, I would like to address situation concerning B-17 on Philippines in 1941, slightly before Pacific war broke out. First of all, we must understand that version of B-17 deployed there were C and D with projected deployment of E version . B-17E was first truly mass produced variant.
Did these early variants had the range to hit Japan ? Well, maximum ferry range without refueling for E is cited as 3200 miles. Therefore, it could be expected that operational range with reduced payload could be around or somewhat less than 1500 miles. It is interesting to note that sites like airwar.ru give higher operational range to D variant compared to E variant. This could be explained by improvements in armor and defensive armament on E version. Finally, we have this official document which gives B-17E max range at 3060 miles (one way) with takeoff weight of 55 000 pounds and 2500 gallons of fuel. On the other hand, distance between Manila and Nagasaki (city in SW Japan) is somewhat bellow 1380 miles. Clark Airfield (where B-17 were stationed) is roughly at the same distance. Of course, B-17 were well in the range of Taiwan (Formosa) and Japanese bases there.
What was Japanese position about all of this ? In 1941 IJN had early variants of A6M Zero which was not much of a bomber destroyer. But IJN would probably not be tasked with air defense of mainland. Their counterpart IJA had early versions of Ki-43 which was even worse in this regard. True, there was Ki-44 but they were not yet operational, similar to Ki-45. Also, Japanese did not know exact range of B-17. They could watch occasional propaganda that appeared in US press and movies like Test Pilot. Their own experiences could have blinded them, because even their twin-engined bombers like G3M had enormous range. In retrospective, US deployment of B-17 to Philippines may have actually pushed Japan towards war instead of serving as deterrence. In a typical Japanese manner, Japanese ruling circles may have deduced it is better to strike and capture Philippines instead of waiting for US long-range aviation to grow even stronger.