So, hypothetically speaking, if someone who knew a bit of Renpy were to, I don't know, enable all of them... think that would break anything? All hypothetical, of course.
Yeah yeah, there's no way in hell I made all my caps 1, who would even do such a thing?
But seriously, when you mess with things like that, they're prone to breaking if not careful, most of the time, games just checks the value of certain variables from my understanding, so if we have two scenes, one where you have to deal with a guy unarmed and succeeds based on your points, and another where you have to shoot/use a blade for some reason, whatever. It would simply check if the mc has the required stats, if you cheated, he will have it in both occasions, and so the successful outcome will happen in both situations, unless the developer makes a more complex check to ensure no cheating which I've honestly never seen, it should cause no problems.
I think problems are more common to occur when you mess with switches, those True/False or 1/0 variables, in all this time using console, I've never truly broken any save in any game I'm pretty sure, as long as you like, take notes of the variables and pay attention to when they're probably used, you're mostly fine