It would seem to me, given missions of long range exploration out in the Federation's "boonies," that all the Enterprise's (really all Starfleet ship's) lifeboats/pods would have a warp drive.
I imagine something like the size nacelles you see on the smallest two seat shuttle pod, stored folded flush into the basic cube shape, post launch they would deploy out on short arms/struts and provide a low warp capability (warp three or four) so the life boat could reach a nearby system with a hopefully suitable planet to await rescue on. Depending on where the abandon ship occurred, rescue might be years in the future. As the ship traveled through the galaxy, the fight computers on the lifeboats would be periodically updated with the location to the nearest class M planets.
In terms of a rescue ship removing people from lifeboats, simply beaming them out would be option number one.
Option number two would be landing the lifeboats on the flight deck, remove the occupants, and if necessary throw the empty lifeboat back into space to make room for the next one. If the original ship was in battle prior to launching the lifeboats, the occupants could be heavily injured and we would see medical teams right alongside the lifeboats on the flight deck.
Option number three, we've seen forcefields hold in atmosphere when the hull has been breached. Docking ports, both male and female, take up a fair amount of room, which would be at a premium in a lifeboat. Have a tractor beam simply butt the lifeboat's pressure hatch up against the rescuing ship's docking port, erect a forcefield tightly around the lifeboat, fill the forcefield with air, open the hatches and transfer the personnel.