Borneo was simply occupied, its inhabitants put under Japanese rule with an iron fist. Murders, rapes, slave labor, deportations all were very common. Wether its under the IJA or the IJN doesn't really matter except harsher treatment by the IJA but that is only a guess. Resistance movements probably experience more casualties against the IJA than the IJN. The death toll on Borneo would have been higher/different depending on the ethnic group or class. Borneo was used by the Japanese simply for resource extraction, mostly oil and slave labour. That was done untill the surrender of Japan, only parts of North Borneo had been retaken by invasion of the Allies before the surrender.