No,modern day identity should not be applied towards neolithic culture.
I think Chinese civilization give or take is around 3,500-4,000 years as I don't believe in Xia or legendary figures.
It is recognized across the world that Japanese civilization is younger than contemporary Chinese and Koreans ones.
Neither is early Japanese history continuous there is no proof Himiko was related to the Yamato bloodline.
Rather Japan was similar to China that there many minor kingdoms(whether or not they spoke Japonic is up to debate) ie Kumaso,Hayato,Koshibito,Mishihase,Emishi etc
Even the Japanese Imperial Household may ultimately have continental origins.
Japan is a land of immigrants and many Chinese and Koreans fled there ie 新撰姓氏録
I don't disagree that immigration from peoples in modern day Korea and China came to the Japanese islands; however, it should be noted that the islands were already populated by proto-mongoloids as seen in the Jomon arts and relics found. Archaeological findings have concluded that Jomon facial make up were mongloid in phenotype.
They were, for all in tense purposes, 'early japanese'.