With A, you cannot sense instantaneous current, only average current. With A, you can also just use one current sense resistor + amp instead of sensing 2 phases.
Average current control is workable and some inverters do that, but I don't see the point when it's not much more expensive to sense the two instantaneous phase currents, i.e., topology B.
I don't see large difference in layout. Just use shunt resistor as small as possible. I have used 1206 SMD parts up to some ~500W power level and 2512 rated for 3W up from there. But maybe the 5kW/48V needs a tad bigger, maybe not. It's about how much accuracy you need; but I wouldn't be scared of using some well-specified x100 shunt amplifiers just to get the resistor dissipation down, and package small. +/-10% current sense accuracy would be more than fine for basic torque control, after all.