The 4-1 joint-second favourite made virtually all in the hands of the trainer's son Sam, digging deep to hold off Lord Du Mesnil and Top Ville Ben, who both tried and failed to go past the game eight-year-old in the closing stages.
That was Good Boy Bobby's second victory of the season at the West Yorkshire track, with his sole loss of the campaign coming in a thrilling finish of the Rehearsal Chase at Newcastle, where he lost nothing in defeat by finishing second to the consistent Aye Right.
The Naunton handler reports Good Boy Bobby to be none the worse for his exertions and is working towards the marathon contest on April 9 with his charge.
Twiston-Davies, who has won the famous race twice in the past with Earth Summit (1998) and Bindaree (2002), said: "Good Boy Bobby is fine, 100 percent.
"It was obviously a hard race (at Wetherby) so we'll give him four or five weeks rest now, then it'll be one more run and onto the Grand National - just don't ask me where!"
When asked to assess Good Boy Bobby's Aintree credentials, Twiston-Davies was fairly optimistic, suggesting now is the ideal time to have a tilt at the world's most famous steeplechase.
"I hope he's a National type. He's quite buzzy so whether he be might just be that little bit too keen, you never know, but he's getting more settled as he gets older so we hope he'll be all right," he said.