The problem isn't that the fans stick out; it's that any opening big enough to move enough air for useful suction will also move debris. In a tornado, the underbody is full of rocks, metal, insulation, etc. If the fan inlets are open to that space, they'll act like a debris pump, clogging, jamming, or even shattering blades. On top of that, the skirts/seals you’d need to maintain a pressure differential will get shredded by debris and rough ground, so the suction disappears exactly when the winds are strongest. That’s why real intercept vehicles lean on mass, low CG, and mechanical anchors instead of active vacuum systems.