This is one of the neat things about Japanese, and actually can shed some light on [音]{おん}[読]{よ}み・[訓]{くん}[読]{よ}み.
One can think about the whole Japanese writing system as just using the 漢字 that have similar meaning for the Japanese word, and "reading" it as Chinese or Japanese.
It started out by being just literal Chinese ([漢文]{かんぶん}). Then, instead of reading it as Chinese, it was read as Japanese (i.e., 漢文[訓読]{くんどく} with [片]{かた}[仮名]{かな} markup). However, after a while, the verbs started being moved to the end (matching Japanese grammar), and then, there was a shift to using the 漢字 for their "sound" instead of actual meaning (i.e., [和文]{わぶん}). Having to write so many strokes just for sound was cumbersome (i.e., [萬葉]{まんよう}[仮名]{がな}); so, [平]{ひら}[仮名]{がな} was invented. It was difficult to understand text written only in 仮名 without the 漢字 to convey meaning; so, after a while, both 漢字 and 仮名 were mixed together (i.e., [和]{わ}[漢]{かん}[混淆]{こんこう}[文]{ぶん} and [仮名]{かな}[交]{ま}じり[文]{ぶん}).
That is a grossly over-simplified history of the Japanese writing system.
So, 漢字 and Japanese sounds have always been loosely coupled, which has allowed for authors to pick-and-match 漢字 and reading.
An example of this is the word つくる—there are different 漢字 used to convey different meanings/nuances.
The author(s) of your Bible decided to use 元始 for the meaning of "はじめ", and 創造 as the meaning of "つくる".