I think I know the answer, but someone may correct me.
Natively calibrating an LCD to its darkest cd/m^2 is by setting it as dark as you can by just using the controls. (i.e. Brightness 0 in the OSD.)
Non-natively calibrating an LCD allows you to go darker by the ICC profile not sending values near 255 to the LCD.
For example, if you had an LCD that natively could only get as dark as 120cd/m^2, but you wanted it to run at 80cd/m^2, the ICC profile could scale down pure white to something around 170/170/170 RGB, instead of 255/255/255. (Obviously different to handle any color cast, and I'm not sure the cd/m^2 scale is proportional to rgb, so 170 might not be the correct number, but you get the point.)
I also believe forcing a monitor to run darker through your profile can lead to loss of detail, although this could be less of an issue if your display takes higher than 8-bit/channel (24-bit total) from the video card. (Most video cards max at 24-bit, some professional level cards run at 30, 34, or 48.) By this, I mean if you want to display rgb 99/99/99 and rgb 98/98/98 next to each other, those *could* visually and measurably come out the same on a display calibrated to be darker through the profile - due to rounding issues.