The wording and presentation in the boarding rules is confusing.
The boarding VALUE of a ship, including multipliers like the MOK are used to work out a vessels BONUS for it's D6 roll to resolve boarding.
In your example it would be
Conqueror: +2 marines
+2 Beserkers
+1 own boarding value higher (24 vs 17)
Total modifier of +5. Roll D6+5 to resolve boarding
Emperor: no bonuses
Total modifier +0. Roll D6 to resolve boarding
highest roll wins and does the difference in scores in damage to the loser
The actual boarding VALUE is the ships current hits. It is this number the MOK would double. If the Conqueror had been boarded it's boarding VALUE would have been 28 (12x2+4) to the Emperors 12, more than double the VALUE, giving a Boarding BONUS of +2, for a total BONUS of +6
I see where you are coming from though, the wording could be clearer, and the method you gave above is what I used to use for years until it was pointed out to me by a GW staffer.
This is how I read it anyway, please post to agree/beat with stick so this can be resolved