The retconned MkVII looks way bulkier then the Older one.
Either the new one is a new design ( MkVII b ), or the Pegasus engineers had to "improvise".
The Pegasus wasn't fully equipped as the Cylons attacked the Scorpion shipyards, and during the attack ( and later during the attack on the Cylon comm relay ( staging ground ), a lot of ships have been destroyed and the Pegasus took also serious damage. Remember - the Pegasus started building new Vipers AFTER they found ore in that Asteroidfield. Pegasus probably
build Vipers before that time, but the amount of parts the ship has onboard is limited and they used them to replace the Vipers they lost in the initial attack.
So it might be, that some ship systems have been "redesigned", they turned out "bulkier" then the standard parts that where used on the colonies.
Just a theory...