[dragoon500ly]

Just some random thoughts...

Rail tunnels (and mines) generally have paper trails that will reveal their locations. Tunnels also have the old rail beds that can still be traced. One tunnel near my home has been abandoned since shortly after the Civil War, and the road bed can still be traced from the neighbouring mountains, this is mostly the blasting work used to construct the bed, but you can see the problem.

To utilize the tunnel, besides a massive purge of records, it would require an extensive deconstruction of the road beds, that will attract attention. IMHO I'd avoid tunnels, at the very least, in the more heavily populated sections of the country.

Mines, especially the older ones that didn't pan out might be a useful alternative, but the drawback is these dud mines, would not have extensive tunnelling, thus requiring major work.

So what to do?

One approach might be to have a university 'sponsor' a new laboratory/experimental station, that for environmental reasons would be placed underground. After several years, the experiment concludes and the university, demolishes the lab for "environmental reasons". Then have a couple of groups of urban explorer's confirm the total destruction of the lab. Move along, nothing to see and here are the YouTube videos to prove it.

Now the Project can move in through a secret entrance and occupy their base.

Another possible use of a tunnel would be building an off-shoot to conceal a bolt-hole or a cache, this would depend on the size of the mountain, of course, another drawback would be future expansion...

Some arguments have been made to use military bases/test ranges for Project construction. With the levels of satellite surveillance during the Cold War, I'd recommend staying as far away as possible!