I would use bed liner. My land is the same color of willow green and i used Rustoleum bed liner for the front and rear bumpers, beneath the trim panels and the roof. Two tone boac and willow green looks great together

 

My 2004 had similar issues, and the seller had the area re-sprayed by a shop for $300. You really would not be able to tell now, unless you look very closely at the windshield seal where you can see the masking edge.

It really shouldn't cost a fortune, and it will add to the value if you ever sell - while Rustoleum will reduce the value considerably.