Don't know unibox, but normally this is the difference:
Physical Vb : the 'real' geometrically measured volume
Vb : the volume the speaker 'thinks to see'.
The filler material (dacron, glasswool etc.) changes several parameters in your box. One of the most important is that the volume seen by the speaker looks greater.
In simple words, airflow is slowed down when passing trough the filler, hence the time needed by a soundwave to reach the end of the box is bigger, like if the box has a bigger volume.
As rule of thumb, for a typical glasswool panel ov 2" you may consider:
Filler on box walls : vol. increase about 10%
Filler on all box : vol increase about 20%
Filler pressed in the box : about 30 %
In reflex enclosures stay with filler on the walls, filling up the box will add other important effects on the vent behavior.
In sealed box you can use more filler, just remember that the Q factor will decrease more than proportionally.
Anyway if the software takes in account the effect of the filler, it should also calculate for you the right parameters.
bye
sandro