I even added a proper airlock to the KH version.

I would suggest the split elevator system is geared more toward security than inconvenience. Even with a small crew, not everyone needs access to the helm.

I would chalk up the lack of a launch to the fact that the scout can make atmospheric landings, not to mention any station can receive one in the docking bay. Why leave the main ship unattended when you can just berth it wherever the launch can go...

"If an assault scout can get in behind a sathar destroyer it has the ADF and MR to remain there and nullify the heavy cannons of the destroyer which are FF weapons. It can regulate the range to optimize all of its weaponry and there by gut said destroyer like a sonic sword through a cybo slug.  In any universe where a HS 3 can consistently take out a HS6 ship, that is not too shabby."

Yes, I agree that the AS needs a deckplan redesign. It should have one lift and the ladder/walkway. It should have a launch or a lifeboat. Maybe it has a collapsable airlock at the bottom.

As for the Sathar, why don't they learn to fly in squadrons of three with one ship mounting a couple more rear-facing weapons? Or have a seeker missile or two to take out those nasty assault scouts?

For starters the Seeker Missile is a MHS:7 weapon system so a destroyer or frigate will not be able to utilize them. They have to be placed like mines, not fired on the fly like conventional missiles. Also noteworthy, any capital ship would be foolish to try leading a scout through said mined area because the missile targets the largest ship.

I never did finish a PT Boat for SF, but I started my "Patrol/Torpedo Gunship" with a HS:4 hull seeing as pirate corvettes can mount a MHS:5 laser cannon so it stands to reason that same hull can mount a MHS:5 torpedo launcher (and limited magazine) along with the standard laser battery.

Also depending on how you interpret canon's clunky atmospheric rulings, it can or can not land in an atmosphere re: "warships of HS:3 or less can land" versus "system ships HS:5 and smaller can land"...obviously flawed seeing as the more powerful atomic drive should allow for that same HS:5 ship to do the same as (or more accurately, better than) its chemical thruster powered counterpart.

Which is exactly why I have the airlock/cargo container mountings aft. Basic aviation skills include determining the plane's CofG and compensating for take offs/landings. As you mentioned, a side to side change is going to drastically alter this, and extreme changes --- such as an exterior mounted extra piece sticking out the side --- could render it useless. Fore to aft changes can be done all day and night without detrimental changes in flight, and extreme changes can still be compensated for to an extent.

How about designing a smaller torpedo that has a shorter range and does less damage, but it will fit the packaging space?

The noteable differences between the two --- the AR does 2d10+4 with a -10 damge table modifier and the torpedo inflicts 4d10 with a -20 modifier, you're more likely likely to inflict double damage with the torpedo and that can guarantee drifting capital ship hulks when it happens, not to mention it's a 360º weapon versus teh AR's forward firing restrictions. The AR offsets this downfall by allowing forward firing bonuses via the pilot skill (along with the head on bonus where applicable), so it is more likely to hit albeit at lesser damage, and ICMs have a tougher time disabling rockets versus torpedos. So one is easier to score a hit while the other guarantees considerably more damage.

One variant I made drops the AR system in favor of a second LB...one on each side. 

A grounded assault scout is probably a dead assault scout when it comes to defending itself whether the turret is on the top or bottom.

Maybe the turret traverses around the ship on a track. Think of the Enterprise from the Next Generation. Its phasers seemed to fire from that half-moon track on the top and bottom of the saucher section. The unseen phaser gun probably rapidly moves along that track to reposition itself for a better aim at the target... or it had several guns there.

That all depends upon what is attacking the scout. If it's atmospheric craft trying to punch a few holes in the hull to prevent it from being spaceworthy (read: pressurized decks), it's a point blank shot for a dorsal turret (re: no penalty to hit). Ditto for ground craft that lack the benefit of natural cover to hide behind (river banks, hills, etc). Re: the rule regarding structural damage needed to punch a hole large enough for man sized creatures to pass through. Return fire from a LB will obliterate any atmospheric vehicle, simply because ship hull points are a far greater scale than structure points...you can punch a hole in each deck via personal weaponry but the scout will still have 15HP...it just won't be able to pressurize the decks once in space --- and arguably the resulting turbulence from said holes could lighten the chances of a successful take off into orbit.

A torpedo fired from orbit, different story...you only get the single defensive shot w/1-4 hex range modifier at the ship firing at you, depending on how far from the planet the enemy ship is...and if that torpedo hits the scout is dusted.

Traveller's Scout Tender did this, albeit with a penalty for the turrets to hit as they traversed the hull to acquire targets. The engineering behind this concept was due to the fact that the tender was "parked" far more often than it was moving, so it could not acquire targets as such without having travelling turrets.