The user should have full control over everything. For example, if the user want to configure it so that all JavaScript time reporting reports that everything t

The user should have full control over everything. For example, if the user want to configure it so that all JavaScript time reporting reports that everything takes zero time, then that is what it should do in that case. If the user wants all timeouts to expire immediately (so that JavaScript-based animations will take zero time), that can also be done, then. You should have enough ropes to hang yourself, and also a few more just in case.