When will people realise there is no 'better' tone?!?!?!?!?!?
People will tell you set necks have better tone than bolt ons. Obviously therefore Strats and Teles are worse than Les Pauls by default. Tell that to SRV, Clapton, or just about any decent player that's used Strats or Teles.
They'll tell you nitro is better than poly as it is thinner. Blind test them. I doubt they could tell.
Some people will tell you that semi-hollow guitars are better than solidbody guitars. The only way you're going to find out is to play both types and make your own judgement. Anyone that says any different is either lying or misguided.
I know that's only semi on-topic, so to answer your question, yes you can use rout straight through the mahogany centre section and glue top and back on.
In terms of guitar building, there are very few right or wrong answers, it's all about what you want, what you prefer, and how you like to do things. It's like wood selection. A guitar made out of solid maple will sound very different to a guitar made out of solid mahogany. Better or worse is down to opinion. Experiment, it's all a form of expression.