*SNIP*
Maybe instead of a boarding variant ,a a boarding pod "weapon"?
Small, medium, large, each capable of launching a pod with different amount of marines.
As PD can take out pods, like missiles, you'd launch boarding pods while the enemy ship is recovering from flux overcharge or EMP effects, or when it's PD is buy with missiles and fighters.
The battle result isn't instant, rather the fight on board takes a while, with pop-up messages telling you progress ("Your marines have pushed to the engineering section of ISS Grant", "Marines report stiff resistance near weapon bay of ISS Grant", etc..). The boarded ship is compromised by the fighting, systems or turrets can randomly shut off and get back up.
The boarders and crew would slowly kill eachother (there would be rolls done behind the scenes). At some point, depending on the force disparity and the remaining enemy forces (ship, not crew) the enemy might surrender or try to blow up the ship. Your marines have a chance to stop this. (so X chance for them to even try, Y for your marines to stop them). However, at that point the enemy will try to sabotage the ship, so the damage it gets ramps up and chances of successful recovery go down
The fight could leave the ship itself unusable, but parts of it can be salvaged. Weapons can be stripped, the derelict itself hauled by a tug and sold to a scrapyard or restored (at great cost)