Yes, the SC has engines intakes on the bottom of the wing.
But they won't have much else but the position in common with the Concorde which has moveable ramps to control the shock waves of the supersonic airflow.
There is no special aerodynamic problems with that intake position - at least no more than intakes on the bottom or on the sides of the fuselage as you see on plenty of military planes.
I wonder more how they (Boeing) are going to fight the FOD problem and water spray from the landing gear. For that reason I would have liked to see a more conventional engine position.
We see at the tail of the SC fuselage along the engines a very pronounces "area ruling", an almost 50 years old trick to delay transsonic drag buildup - as first seen on the Convair F-102A Delta Dagger and the Republic F-105 Thunderchief. That area ruling would probably be difficult to produce with a more forward engine position. A pressurized passenger cabin with a wasp waist would certainly be some extraordinary enginering challenge, and not a very practical thing to arrange seats in.
Regards, Preben Norholm
Always keep your number of landings equal to your number of take-offs