The study you're referencing is looking at paternal lineage of Israelis born in Israel, not the ancestral lineage of all Israelis.

A second-generation Israeli would be considered 'From Israel by paternal country of origin" in this census, because their paternal country of origin would be Israel.

The bulk of immigration happened in the 1950's-1970's. The number of Israeli's who's ancestors lived in Israel before the establishment of the Israeli state isn't a known or studied figure a definitively answered question, but it's reasonable to assume that it's a minority given the large migrations that happened during and after the Nakba.

The only real information we have regarding the make-up of Palestine before its partitioning are a couple of censuses done during the British occupation, but it was during a period of time when zionist jews were already beginning to migrate. Here's the topline:

The census found a total population of 1,035,821 (1,033,314 excluding the numbers of H.M. Forces),[2] an increase of 36.8% since 1922, of which the Jewish population increased by 108.4%.[1]

The population was divided by religion as follows: 759,717 Muslims, 174,610 Jews, 91,398 Christians, 9,148 Druzes, 350 Bahais, 182 Samaritans, and 421 reporting no religion.[3] A special problem was posed by the nomadic Bedouin of the south, who were reluctant to co-operate. Estimates of each tribe were made by officers of the district administration according to local observation. The total of 759,717 Muslims included 66,553 persons enumerated by that method.[4] The number of foreign British forces stationed in Palestine in 1931 totalled 2,500.[5]