The target tracking is 100% software-based -- where DJI GO is following the target by analyzing the image that is displayed in DJI GO. If the image is too dark on the screen in DJI GO (even when using no filters) or it's too dark in the flying area, the target will not be found. It does a pretty good job of finding the target even when the exposure is not set properly. For that reason, I don't think using filters is going to negatively impact this feature. The OP might have a problem if doing something odd like using an ND64 filter after the sun has set. That shouldn't be a likely scenario for most people though.
Right -- the front sensors are only going to be used to avoid the subject.