MEMES_R_gud
Just use the system as a measure of strength and skill. If you do have stat points you could do something unique, where instead of the stats giving him strength when he uses them instead they unlock the ability to develope to that strength. Basically if he has a strength of 7 and has no natural way to reach higher the stat point would allow his body to naturally become that strong through training/combat. Basically stopping him from becoming god by adding points and makes him less suspicious (if he suddenly gains super strength they might be more curious how he did that thwn if they see him training and becomeing stronger over time also having a mature mind that they can just sum to trauma). I hope my ideas help the story.
a way to make it so that it doesn't affect the story much is that he can only increase the stats artifically by decimal points like by 0.1 per point and that he can't put say put 10 points in a stat at once. you can also make it so that the larger the stat the more points needed to make that stat higher. one thing that you can do that would probaly help is to make skills that he can learn, such as shooting(Rifles) or CQC(UNSC). the words in the parentheses being the specifics that the skill would work on and that he has to continually use and practice to raise the skill level. this should help you