I definitely vote covering rivet spots and molding into the body so it looks factory.
I'm partial to the clean, almost factory look.
2004 SVT: Boost soon!
2010 Ford Escape 3.0 V6
2004 F350 6.8L V10
1986 XR4Ti 2.3L Turbo, 15 psi
2007 ST ; formally bewst'd - R.I.P