Why reference RF on L1 to L3?
There are a couple of reasons to do this.


You often have things like high speed digital lines on the top layer that you want to be thin so you can fit them and want a sane impedance for them (often 50R) so you need the layer stack to give you that as L1/L2. However your RF line is somewhat lossy if you make it thin, mainly a skin effect thing at high frequency, so a larger line geometry is indicated. 
It is helpful if your RF line and the geometry of pads required for connectors and component footprints more or less match, it avoids lots of faffing about with relieving grounds under caps and  resistors. An 0603 cap for example will have a footprint that to match the width of its feed line needs a fairly wide track.
Sometimes dielectric losses are a concern (mainly at power), more spacing means less heat in the substrate.