Did you ask your LBS to change crank length? Most will do that for no additional charge.
As for re-configuring the lever position your LBS should do that for you at time of purchase.
The stock saddle is usually a throw away, the LBS I worked at gave a 20% discount on saddles with new bike purchase.
Cable line on downtube, now you're getting picky. That configuration is very standard because it's cheap. I haven't seen a new production frame with anything else but the plastic solution. Plastic bolt-on guide replaced super-cool braze-on guides a few decades ago.