As for the V-jet, I don't know why they used a V-tail. It appears to combine the suboptimal access of buried engines with the structural awkwardness of ring spars required to react bending moment around each engine, and then tops it off with a generous helping of intersection drag. At a guess, I'd say they did it that way because they could, and because the Williams guys footing the bills (with Uncle Sam's help) thought it looked awesome radical way kewl.
Oh, yeah, there are also sometimes observability issues, as on the F117. But that's on a way smaller wavelength.