Ah, very helpful. Looked at the grappling section of the combat rules but didn't see any bonus formula listed. Of course, I was very tired at the time.
So, I've got two ship designs almost statted out, and it occurs to me I have the money to buy both of them. I might do that, but first, I wanted opinions about what's more useful for starships in this system.
My first model is a custom interceptor, it's smaller (Huge), faster (better speed, initiative & Dex/Reflex Save), and has 1 more emplacement point, but it's shields, HP, and Str/Fort Defense/Threshold are lower. The other is a custom superiority fighter, with much better shields and improved HP, Str, ect, but it's larger (Gargantuan), significantly slower (4 less initiative and ref defense, -2 squares speed), and has 1 less emplacement point. Other stats are more or less identical between the two, I'll post the blocks in a minute for comparison.
Both ships are probably going to have Sensor Baffling and Sensor Mask, allowing them to make stealth checks with a +10 bonus without requiring any kind of cover, and are generally designed for a "disable the enemy from hiding" approach. So would it be better to be fast and agile, or slow and durable?
Two more questions:
1) Can I select the "double weapon" option for the prototype benefit, and then swap the second weapon system with a different one that uses the same number of emplacement points, paying the difference in cost? Or would I have to pull it out afterwards and replace it?
It's basically the difference between getting full value for the cloned weapon, and having to sell it at 1/4 cost instead, which doesn't mean much when you're walking around with 1.2 mil in your pocket.
2) I take it space mines just use their own attack bonus, and are unaffected by the ship or pilot's attack boni?
[edit] Stats for the two ship designs:
QUOTE (Custom Interceptor)
-Sabotuer [Gaanaylir Jorir]-
(Huge Starfighter)
Size Modifier: -2
Init: +6
Perception:
Ref: 23 (15 flat footed) +7 pilot level (+3 armor)
Fort: 25
HP: 90
DR: 10
SR: 15
Threshold: 23
Speed: 16/7
Ranged: +5 double medium ion cannons
Ranged: +5 proton torpedo launcher
Ranged: +10 advanced space mine launcher
Fighting Space: 3x3 or 1 square (Starship Scale)
Cover: total
Base Atk: +5
Grp: +18
Atk Options:
Str: 40 +15
Dex: 26 + 8
Con: --
Int: 20 + 5
Initiative: +6
Mechanics:
Perception:
Pilot: +6
Use Computer:
Crew: 1
Passengers: 0
Cargo: 25 kg
Consumables: 2 days
Carried Craft:
Payload: 3+ Proton Torpedoes
4+ Advanced Space Mines
Emplacement Points: 1
Double Medium Ion Cannons (pilot)
Atk +5
Dmg 6d10x2 ion
Proton Torpedo Launcher (pilot)
Atk +5
Dmg 9d10x2 4-square splash
Space Mine Launcher (pilot)
Atk +10
Dmg 9d10x2 4-square splash
QUOTE (Superiority Fighter)
-Dread Not (Chab Nahs)-
(Gargantuan Starfighter)
Size Modifier: -5
Init: +2
Perception:
Ref: 19 (12 flat footed) +7 Armor
Fort: 27
HP: 120
DR: 10
SR: 35
Threshold: 45
Speed: 16/5
Ranged: +5 double medium ion cannons
Ranged: +5 proton torpedo launcher
Ranged: +10 advanced space mine launcher
Fighting Space: 4x4 or 1 square (Starship Scale)
Cover: total
Base Atk: +5
Grp: +17
Atk Options:
Str: 44 +17
Dex: 24 + 7
Con: --
Int: 20 + 5
Initiative: +2
Mechanics:
Perception:
Pilot: +2
Use Computer:
Crew: 1
Passengers: 0
Cargo: 25 kg
Consumables: 2 days
Carried Craft:
Payload: 3+ Proton Torpedoes
4+ Advanced Space Mines
Emplacement Points: 0
Double Medium Ion Cannons (pilot)
Atk +5
Dmg 6d10x2 ion
Proton Torpedo Launcher (pilot)
Atk +5
Dmg 9d10x2 4-square splash
Space Mine Launcher (pilot)
Atk +10
Dmg 9d10x2 4-square splash
These aren't the full stats, mind you--just the things that directly affect which ship is better. I might throw in customized controls on both of them just to get that extra +1 to piloting.

[edit2] OOH! Shiney!
I just checked the rules for hardpoint modifications. It says one hardpoint mod gives you 4 hardpoints, which can each hold one missile, mine, or torpedo...
...
unless it's a weapon restricted to ships of Colossal size or greater, in which case it uses two of the 4 hardpoints instead of just one.
Soooo, does this mean I can use hardpoints to strap a pair of heavy concussion missiles to my starfighter?