The exposure meter does not calculate how the taken picture will look. It shows you how bright your picture will be, based on what the sensor sees, it does not calculate the flash.
You should consider learning some basics about photography before using the manual mode.
With the build in flash, exposure for portraits in near darkness should be set around 1/200-1/250 second.
Also, I don't recommend shooting portraits in the dark in general.
I a nutshell:
If you shoot photos in the dark, the automatics wont really work and the exposure meter wont really work. You will have to know exactly what you are doing.
The build in flash is not really good, it is mostly meant to trigger external flashes. If want to take portraits in dark environments often, I recommend buying and external flash like the SB-700.