As far as we know "China, Japan and Korea" have been approximately (for the latter two exactly), where they have been for millenia and did originate in the general area of theirs. I do not know how to answer a question like this via a historical explanation, whether a group of people is considered "native" or not or if it counts as "native" if the preexisting group of people were driven away or have been assimilated into the corresponding cultures of that region. From a linguistical standpoint, previous proto-languages of the three linguistic groups did not "colonize" the regions they moved into, but migrate as a whole as you cannot assume why they did this.

I cannot further add on to Chinese history, as the origin of the Sino-Tibetan language group is presumed to have originated either around the Tibetan plateau or modern day Burma, but ancient China was historically much more fractured than it was during the post late-medieval era, being split up into various kingdoms, who may or may not have spoken a Chinese language (Such as the state of Yan in modern day Northern China, which was found to have features of bronze metalsmithing also appearing in the North East Asian cultures). Instances of ethnic deportations did occur, one mentioned in the Sanguozhi following the defeat of the Kingdom of Koguryŏ by the Tang dynasty, where around 100.000 people were deported to the area around Xi'an.

As for more modern history of China, there have definetly been instances of "colonization" and displacement of various people, most notably in the regions of Inner Mongolia, Manchuria, Turkestan as well as Tibet, where a previously non-Chinese majority was either completely assimililated (As is the case of Manchu) or became a majority Chinese area, though it wasn't previously (Turkestan, Inner Mongolia). There the distinction between the Huang-He rice farming civilization and the non "China-proper" regions is made, as these are not part of the core Chinese history, that revolved around the fertile plains of Central China, spreading outwards over time.

As for Japan, there was likely a previous population of hunter-gatherers, who likely only numbered in the few hundreds, if not several thousands until the first millenia BC, when the start of the Yayoi migration occured (due to unknown reasons). The ancestors of these people did likely cross the back then existing land bridge that connected Korea and Japan around 8000 BC. The "Emishi", ancestors of today's Ainu remained until 900 AD on the northern part of the main island, until they were driven of by the Yamato Wa to the northern island of Hokkaido.

Korea was the origin location of the aforementioned Yayoi, also controversially referred to as Peninsular Yayoi (problematic, as they were made up the ancestry of the southern Koreanic as well), who moved to Japan subsequently after the migration of equestrian (?) proto-Koreanic people arriving from Siberia. Not much is known about this period, referred to as the three Hans in Korean historiography. It is not known whether the "Jin-guk" confederacy was a Yayoi or one of the arriving Koreanic entities. The proto-Koreanic tribes of Ye and the Maek are the supposed founding people of the various Koreanic kingdoms afterwards, predating the Three Kingdoms of Korea.

Parallel to this is the first Korean "state" of Ko-Chosŏn, which was a semi-theocratic tribal kingdom that existed around the mythological capital of "Asadal" (supposed to be around modern day Pyeongyang).

One controversial aspect of this is the southern central part of Korea, where the so called "Kaya"- Confederacy existed, a grouping of smaller towns, that is disputed to be either Koreanic or a Japanese colony named "Mimana".

Source for population numbers: McEvedy, Colin. Atlas of world population history. Penguin Books Ltd, 1979.