Well, there are multiple reasons, like "it's a good film" and such. But the main reason is that there is a character in it called Petey. He's one of Farmer Bean's lackeys, and he's voiced by Jarvis Cocker.
And rather than make up his appearance, they just made the model look like Jarvis Cocker.
This is a film with a stop-motion Jarvis Cocker in it.
And yes, he's holding a banjo because he sings a song at one point. Then Michael Gambon (Bean) shouts at him.
Me and my friend Phil sincerely hope Jarvis was given the model after filming finished and it now adorns his mantlepiece.