PCB layout of buck converter: capacitor placement
There is a lot of ripple current in the input caps in a buck converter.  However, if you have a good solid ground plane you don't need to worry about "frequencies of several hundred MHz being loaded on ground of input."  Further, your large output caps will have a self-resonant frequency below 100s of MHz and will essentially be inductive at those frequencies.  

In all the many hundreds of buck converters I've laid out or looked at I've never seen a problem where input ground noise couples through the ouput cap's ground to the output.  Many of these had a close low-inductance connection between input and output caps.  Where are they suggesting the output reference is anyway? Wouldn't it be the negative terminal of the output cap?

This is not to say that ground noise can't be a problem.  Poorly designed grounding schemes can absolutely lead to a noisy output.  It's just that tightly coupling the grounds of the input and output caps is not a problem in my experience.