My understanding is that not everyone was comfortable with Mechanicus fleets just getting to purchase the set of upgrades they want, since you would see a lot of fleets "stacking" only one or two key upgrades. In some ways this is both a mechanics and fluff issue, since on the one hand it helps with game balance but it also helps represent the way no two Mechanicus ships are exactly alike (on account of their Magos' personal quirks).
A compromise was reached wherein the tables were modified such that "weaker" results on the original FAQ 2010 version were improved or replaced, in an attempt to bring parity to the different Mechanicus Gifts. In addition, BFGR changed the upgrade allocation system from a random, per-ship roll to the following:
At the start of the game:
-For each ship that rolled a '6' for its Ld value, pick one gift and add it to your "pool" of gifts.
-For each other ship, roll a D6 on the table and add the result to your "pool" of gifts.
-Assign each gift to a single ship as desired, until every gift in your "pool" has been allocated.
This was BFGR's attempt to fix the issue of wild power swings due to random generation (e.g. getting upgrades on ships that can't make good use of them), while still holding back on letting players go wild with every ship having Augmened Weapon Relays.
I believe it is discussed somewhere in this thread:
http://www.forum.specialist-arms.com/index.php?topic=4948.0