The E46 SMG is a pretty heavy clunky piece. As far as I know, the actual gear box casing is significantly different than the 6speed M3 gearbox and wouldn't be modifiable.
Swapping a 6spd into an E46 would also be a bit of work, but doable. You'd need (minimum) the cross-brace for the 6spd, the linkages for the shifter, the shifter console mount + bushings, clutch pedal + bracket, slave cylinder + pipes + hoses, clutch, flywheel, prop-shaft.
I am not sure if the E46 by default, contains the necessary wiring harness to accomodate the 6spd. I would highly doubt it and therefore suspect you'd have to modify the wiring harness to include the clutch switch and reverse gear sensor wiring, as well as deleting/removing the SMG control module, pump and harness. The DME (BMW code for ECM) is also specific to the SMG model so that would need to be replaced as well.
Like I said, this is the minimum amount of work needed to be done. It would be cheaper and far easier to find a very nice condition 6spd E46 and move on from there.