Your recommender will have to include ‘predictions’ of your likely scores, at the same time as you submit your application. If the predictions are for less than 40 points your application will be closed and denied*. If the predictions are for 40 or more points, your application moves to the next stage of evaluation.
If you then get an invitation to interview, and following the interview get a conditional offer, that offer will specify the number of points you need to achieve, and (as appropriate) any specific sub scores. When you get your score results, if they meet the offer you send them into Oxford and get your full, formal, unconditional acceptance. If they do not meet the offer you most likely will lose your offer.
So the question is: will your recommender say that you are likely to get 40 points? And how uncertain are you about achieving the 40?
*unless you are a UK student for whom contextual evaluation applies. Also, Cambridge may accept you If you are on your country’s national chemistry olympiad team.