I don't think tracking is software. My guess is that in "covering" the IR sensors they used too thick of a IR-transparent plastic around it so it blurred the laser hits which ended up with bad timing data.
The Vive looks pockmarked like the lunar surface for a reason. It doesn't use IR transparent plastic, instead every single sensor has a little window with a covering on it to let unblurred laser hits. If PiMax ships with the current plastic there is no doubt that many people will take it apart to drill some holes in it for improved tracking, but my bet is that they will either go with windows, or redo the molding to have the plastic be very, very thin where the sensors are and have the sensors extremely close to the internal of the plastic.