Notes:
Units can not carry cargo or capture ships via boarding parties... Allegiance subverters would work, but are insanely powerful skip-all weapons that would stack the chance to convert (even at 1% chance, 100 fighters in a stack will get you 100% chance to convert.
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You will want a small ship with boarding parties instead. If you put the boarding party ability into the hull, the ship will never lose them, and can capture an infinite number of ships in combat.
A special mount that reduces the size or cost of boarding parties on the assault transport would be effective.