When spending Design Points it shows the total number of points the car has in each area. If you have bonus points from your Engine/Tyre/Fuel Supplier then it will show as being above 100 points. So if you have a +3 Acceleration bonus you can develop your car to have 103 Acceleration.
On the overview screen, however, it will only show 100 as a maximum. Does this mean you no longer get any benefit from the bonus or is it that the game just doesn't display the extra 3 points on the overview screen. Perhaps it is worth stopping development at 97 points, having the 3 bonus points to top it up to and spending the remaining DPs elsewhere?