[GuidoK]

Boost is pretty linear to torque. And the torque curve is pretty linear on the m54. Only after 5.5k or 6k it noticeably starts falling off a bit.
Torque on 2,5k or on 5k is pretty much the same imho. Certainly not that of a difference to not choose for a specific type of supercharger.
A few Nm are not going to give the difference in snapping driveshafts or not. Certainly not if considering that to my opinion an engine can handle more torque in low and midrange than in the high range. Unless you spec a supercharger that only gives boost after 6k rpm. But's what's the use in that?
ESS specs their twinscrews up to 15psi on the m54 without much trouble on the stock lower block (only low compression pistons. driveshaft and rods stay the same). I don't see potential problems.
The problems I do see are maybe on headbolts and gasket, but that's also very revdependant, as cooling/heat also plays a role in that. Those are usually blown at higher rpms.