I found a interior cell called zUnusedCellar02 which I decided to use as the basis for a new mod. I've created a secondary HQ / Sub HQ or fall-back HQ for the railroad. It's not huge, but had the sort of things that you expect a fall-back HQ to have;
A main command room with maps, chalk boards, some desks, a ham radio, control computers and a rest area.
A small room with bunk beds, a kitchen, lounge and supplies.
A bathroom with shower and toilet.
An infirmary.
Work space.
An entry way.

The key can be found in the Rail Road HQ. See the screen shot. The entry is sneaky. Very sneaky. It's in Parkview Apartments. Very very sneaky. If you have trouble finding it, put your pip boy map on local view.

I've tried to keep it Lore friendly. Yes there's heaps of ammo down there, and a few heavy guns, but if you fall back from your main HQ it means that's lost and you'll need some guns and ammo to regroup. 

I've updated this file to now include an escape tunnel, and a second small bunker up north at Leonard Moore's store as a safe house for Rail Road agents with escaping synths. 

100% of donations for this mod go to the Ukraine Relief Fund.

The usual FAQ:

Q. Is it okay to add to the game at the start / end / some other time?
A. It is okay to add at any time in a game.  But ideally it should be added before you encounter the Rail Road.

Q. Does it break quests?
A. I highly doubt it. 

Q. Does it break pre-combines?
A. Possibly, but it does not seem to affect game play.

Q. I found an issue / floating object / something that needs fixing.
A. Great, please take a screen shot of it and let me know.

Q. Does ....
A. Hey, I'm just an autistic person from Australia who makes mods. I don't have all the answers. Extra changes are fee for service. This is not a joke. I'm tired of people whinging about stuff they can't do themselves and then demanding I make this change or do that and having a sense of entitlement about it. The mod is provided AS IS. I will fix bugs, and that is it. If you harass me for other stuff I WILL block you. No I will not make ESP files or do stuff about pre-combines. I tried in the past it was so stressful due to people nagging that I stopped making mods for months. Now I just make mods for me and publish them here if I feel like it. This means I will not modify my mod for people's whims unless they pay me for it, including paying me to spend time training up on how to do things. And seriously, all the people whinging about pre-combines, no, just no. I will not stuff around with that crap after spending days trying to learn this "simple" thing only for it to be too hard. Don't even ask, you will be blocked. Sorry for the bitterness, I need to focus on living my life for my enjoyment, not the pressure of others.

Q. Hey, I still want "this mod" to your mod and I have the technical know-how to make that change. Can I make the change to your mod for you and you release it here?
A. YES! By all means. If you want to mess with the pre-combines of make and ESP file for me, by all means I welcome that. I am happy to help others who are willing to put the effort in.

Q. I don't like your mod because .... / I want to tell you you're wrong!!! / I want to argue with you!
A. No problem, scroll on and download another mod. If you be rude, argumentative or disrespectful I'll just ban you from my mods then block you. Please just don't. I'm very autistic and can't handle conflict. Seriously, people don't seem to get this so I've now banned over a dozen people for being disrespectful, argumentative or entitled and demanding.

Q. Do people really ask you these questions?
A. You better believe it.