Builds that take advantage of unintended interactions should be fixed, and a system that hides them or penalizes players for a bug would be a bad system.
Of course. The idea is to create a system that eases the burden of fine-tuning the balance and leaves the problem-solving to the developers.
A skill that no one uses despite having a huge bonus is a skill that the developers should fix or change. It’s a good way to find those skills that no one wants to use, no matter how powerful they are.
Additionally, bonuses that remain stable over time would be indicators of a necessary change in a skill and how much it needs to change.