I only noticed this because of my home-brew units and the latest versions of MegaMek supporting Alpha Strike record sheets. The basic issue is that Fore Sides have their bay factors put into the Fore arc in Alpha Strike. So an optimized "corner-posted" design in the regular BT rules ends up with anemic broadsides and an over-strength nose.
As a baseline, take a look at the battleship we all know and love, the McKenna. Because it's HNPPC batteries are split (3) Broadside and (3) Aft-Side, it's consolidated Left/Right arcs in Alpha Strike are 360 damage, same as the ship's extreme range broadside firepower of 6x60pt bays in the normal game.
Now without dipping into fan designs too much, just image you re-arranged the McKenna by moving the LBS/RBS HNPPCs into the Fore-Right/Fore-Left. With vector movement in BT, this ship would still have a 360pt extreme-range broadside because the Fore-Left and Aft-Left arcs overlap considerably, and you can easily point your side towards the enemy while maneuvering in a different direction. But the Alpha Strike ship would have only a 180pt broadside. The 3x60 = 180 damage that we shifted to the Fore-sides is combined entirely into the AS Front, which actually gives the Front Arc 360 damage at extreme range from HNPPCs! This often makes the Nose the ship's most heavily-armed arc, which means you should be pointing the front at the enemy instead of the side. If the corner-posted McKenna tried to sit and trade broadsides with the canon McKenna in Alpha Strike rules, it would get clobbered pretty consistently; the canon design has double the throw weight at 360 vs 180 damage.
Long story short, a corner-posted ship might have particular tactics in mind when designed, and yet in AS trying to use the ship the same way could turn out very badly. My only suggested solution would be to at least split the Fore-Side bay damage 50/50 into the Front and Side Arcs to reduce the severity of the effect. I just find it frustrating as someone who would like to use slightly-more-abstracted rules because I want to play fairly large space battles with my custom designs. Designs which of course have a lot of thought/optimization put into them, their concept of employment, and my overall desired fleet tactics...... which doesn't manifest in their AS stats.
