Riiiiighht. That’s why the boat is riddled with bullet holes. The only reason the punk survived is he was shielded by the engine.
Look closely at the boat. It is not riddled with bullet holes is it? And there aren't many indications of bullet damage in the boat, are there?
Now look also at the location of the boat relative to the driveway and the fence and driveway next door. The article shows LEOs at the front of the house, no doubt many more were present there once they were all in place. The area behind the garage was cleared of officers early in the action to allow fire from the front of the boat. Clearly firing on the boat from both sides was possible, and even fire through the wood fence next to the boat from a concealed position, or even an armored vehicle in the neighbor's driveway.
And yet you are suggesting nobody from FBI HRT, or any other SWAT team present could hit the terrorist because he was behind the engine? Not really. It looks like they carefully fired a few rounds into the boat, maybe even with low penetration ammo. Even the bullet holes present do not seem to be matched with exit holes on the far side. I'm willing to bet that a standard 5.56mm round will go right through a fiberglass boat and its wood trim.
The search operation may have been poorly planned and a failure, but the final capture operation was very well done.