Actual implementation, IMO, would be much harder. Unless the whole capture/boarding mechanic is translated into real time battle, or if ships kept track of exact specific crews it carried in combat, I just don't see it functioning well.
Tracking your Marine and Crew numbers, yes you would have to do that. What happens when your crew numbers dwindle in combat? Your ship starts to move a little slower, shoot a little slower etc. by percentages below your optimal crew amount. Until the crew reaches zero and the enemy start manning the ship themselves. If they can put enough man power onto the ship they could even use the ship in the remainder of the battle. If we're using marines though you might want to make it so they operate the ship less effectively until battle ends though.
Choosing to have ships full of marines to board other vessels is risk enough in a combat situation. Right now there is no link between combat speed and armor that I know of. If a ship has more armor it should generally move slower so there will be different types of troop carriers - fast ones, slow ones with more armor etc. If you want a armored troop carrier to go faster maybe it unloads troops slower. The possibilities are numerous.
When a troop carrier docks with a ship 100 marines don't just instantly undock onto the enemy vessel. They invade the vessel at a fixed rate while they do battle with the ship's marines/crew. If someone blows up the troop carrier on the side of that B.Cruiser it is attached to, the marines left inside it die. It will be the only tactic besides drones where someone can actually blow up your firepower (marines). Capturing an entire Hegemony fleet would be unrealistic, you would be far too defenseless trying to field a fleet composed completely of troop carriers. Troop carriers might not be as nimble as frigates (usually), so that makes frigates and quicker destroyers the natural counter to troop carriers. Even
IF they manage to attach themselves to your capital ship, armed with a pd laser sitting there they are pretty defenseless. Making this tactic situational and rewarding if mastered.