Well poop! Houston, we have a problem! It's been a long time since I actually played the main quest at PL, and I forgot that there is a huge hidden door that takes up a BUNCH - like MOST of the open floor area at the bottom of the lighthouse. Once the door is open, there's not that much room on the sides to put a bed, tables or much else. This could be the reason why it hasn't been done by now. Also, it seems that Smugglers also live there, and I was attacked outside heading up the path, and inside I got pwned by one WAY above me with a rocket launcher while I was trying to kill the other 2 shooting at me, lol. Personally, I don't like to have to fight my way into my own house, lol.
If it was straight up just adding a bed and such I could almost have it about finished by now, but this spot might be better off left vanilla, especially as buggy as it is messing with vanilla cells & their objects. An ambitious modder might do a complete overhaul, and to get it right that's possibly what it would need. It would be a lot of work.
I took some shots of the door in the floor: http://ypdesign.com/fo3/tent/lighthouse.htm Could I interest you in a cleaned up admin tent? The other pics on that page are of a quick tweak I did a while back on the admin tent. If you want it, I'll upload it and give you a link. It's not released or anything but if people want it, I'll release it.
The smugglers are not there at the start, they randomly start spawning there during the game, so you could change the script that makes them spawn and just reword it so they aren't enabled during the game.
And for the door in the floor, I guess you could try adding in an electrical switch that's scripted to open the door when the player wants and not just open and stay open during the MQ, (there's a script that opens the door in the MQ, just kill it and attach one to the switch that changes the door instead.) then put wood planks across the edge of the door opening so that they are not visible when the door is closed, but they allow the player to walk across the opening when the door is open. Or just remove the script that opens the door in the MQ, and put in a hatch in the floor that loads the Medical Center and changes the door in the underground place to load on top of the hatch.
(The above suggestions are assuming the GECK works like the Morrowind and Oblivion CS, if they don't work in fallout, I would just delete the smugglers and replace the big door in the floor with a little hatch in the corner.)
I would do this stuff myself, but I don't have the GECK.
Edit: the wood planks I was talking about may have been a bit confusing. Here's a diagram:
________
1///////////1
1///////////1
1///////////1
1///////////1
1///////////1
1///////////1
1----------1
1----------1
1----------1
(it's from above, the slashes are planks, the hyphens are open space, the player can still walk down the steps, but now the space above the steps can still be used for furniture.)