Yes, most freight in Japan are handled through trucks instead, but there are no road tunneos between Honshu and Hokkaido, so their only options are trains or ferry.
Also, for all the remaining freight services in Japan, freight trains do share track with passenger tracks, but unlike North America, they are freight trains using passenger train company track instead of reverse>>1587603
The alternative os ferry transportation of all freight and let Shinkansen take up the entire tunnel. But the econonic damage to Hokkaodo have been deemed too great for such act to he even worth considering>>1587604
Would still vulnerable to the same mechanism>>1587534
It might actually be the same train afterall but just people are being required to deboard from the train
According to my understanding,
First of all, some of those who make through journey from Tokyo into Ome area might take other trains instead, thus freeing up space for Tachikawa-originating passengers
Second, even if some still take the same trains, they will still be forced to deboard and let others waiting at the platform to board first, making seats available to passengers waiting at the station