"Doesn't the defense also have a burden to explain the duct tape, the stench, etc.? Has the defense met that burden?"

In law, there is no such burden. It doesn't matter. The only thing the defense must prove is that the prosecution failed to prove their case. And 12 jurors who spent far more time in the courtroom than either you or I agreed that they did not. And did so quite quickly, as jury deliberations go. But the prosecution had no murder weapon, so solid motive, and no time of death. From what I've read (which is admittedly limited) they even did a poor job with cause of death.