I have a few loose screws too.
The socket head that held my gas tank to the steering head was loose when I got the bike too. I kept noticing a thump sound as I went down a bumpy road. It was the almost empty tank biuncing. I put a little Loctite 232 Threadlocker on the threaded part and tightened it down.
Oil filters are put on with a dry gasket at the factory and are a real bugger to get off the first time. The first time on my Bonnie necessitated a screwdriver through the casing for added torque.
One thing about the bonnie is that the sump extension casting is a thin wall, pressure die casting and over torquing the drain plug will crack the casting. That's well documented elsewhere. The sump pan on the R3 seems much more robust so it should take a bit more abuse.
In as much as the bikes are assembled on a assembly line, at each particular assembly station, pre-set air torque drivers are most likely utilized on the fasteners. It's not economically feasible for someone on the assembly line to use a torque wrench on each fastener.