@GillesHuizinga Welcome, Gilles. The short answer is yes. If you cut through your work piece, you will cut into the spoil board. The longer answer is, if you zero on your spoil board, you can keep the cut into the spoil board extremely shallow. Look at this video:
If you want to zero on the material surface, the key is to make sure that your spoil board is thicker than the T-track is high. Generally, you would use 3/4" mdf for your spoil board. T-tracks are generally 3/8" high. So, you have 3/8" to play with before you hit the tracks. There is no reason at all to be cutting 3/8" beyond the thickness of your work piece, so you will not hit the track. Of course, every time you re-surface your spoil board, that margin decreases.