Of course the fines are punitive, that's because the fines aren't supposed to be a revenues source for the EU they're supposed to deter behaviour (To the point the first round of them are often dimunitive or waived entirely before ramping up steeply if the behaviour doesn't change).
Another reason the fines are based on global revenue are to get around all the income shenanigans tech companies play, or do you really believe google's most profitable country is Ireland?
>Apple has less than 30% market share globally.
The EU is less than 30% of the population globally, and only 10% of iphone sales. By your logic clearly what it does doesn't have an outsized effect on apple that needs to be corrected.