Marine Officers got a massive overhaul in how they manage your marines. They can now distribute marines among the ships in your squad, taking the drone slots of the ship.
You'll then see your marines in the ship, and repeat the process as many times as you'd like.
You may initiate boarding like vanilla (select target-Board) or hail any of your ships with marines. Use options Attack-Start Boarding of...-Select target.
All marines in the skunk and all ships with marines will deploy their boarding pods. Ships will fly to a reasonable distance before dropping their pods and boosting away. All marines will participate in the battle, all gain experience, and share casualties.
You must hail any of your ships and use Attack-Start Boarding of...-Select target. Once you pick your target station, the procedure is the same as boarding a ship, but with much more boarding resistance. Many enemy stations will abandon themselves after hitting a lower hull threshold, and will be easier to capture. Your MO will be an absolute boss and coordinate repair of much of the station upon a successful boarding, so don't feel afraid to help convince the current occupants to leave before starting your assault.
In both cases, you may choose to fight for an allied faction instead of yourself, which will turn over the newly acquired ship or station to the faction of your choosing after your victory. Cancelling a mission may sacrifice your MO, or hurt your marines. Reloading a save during a boarding will end the mission and you will lose your MO.