If there wasn't a penalty, everyone would likely field a VBB of some kind rather than your base BB. In a typical game, you are only going to see max two battlebarges. With the standard BB 425 points, you have a huge range of options that are cheaper and would bring heavy lances or other weapons to the fleet even with the extra 35 points for the marine crew. Take for instance the desolator, for 335 points (90 points cheaper than the BB) I can bring s8 (p/sb) 60cm lances, 5 cm better speed, an extra shield and turret, and spit out 9 torpedoes. There needs to be some drawback for fielding something like that in the marine fleet and the VP penalty does this.
Other examples would be an apocalypse for 400 points (25 points cheaper and can pump out a NC and six 60cm lances per side LO) or Emperors for 400 points, etc.