Hi, Mike, and welcome...if a little late for me to do dat.
The way to think about under-mountain access, very seriously, is to plan for no derailments under there. That means flextrack in as few joins as possible and on well planed roadbed that is, itself, well fixed in place.
You would use one sliding joiner at one joint between two lengths of flex, ideally, although even better would be one 3' length for the whole tunnel. But the one or two joins with metal joiners would not be soldered so that the rail ends can accommodate the movement of the bench below them due to changes in humidity and, in some rare extreme cases, in temperature. Humidity in wooden benchwork is what generates about 85% of any measurable change in the track gaps.
Secondly, every rail end must be dressed with a metal file to slightly bevel the top leading surface of the rail head, and the same must be done for the flange face of the rail head. This slight ramp on the two faces practically reduces the odd mishap due to flanges being lifted by sharp cut edges to zero.
Use caulking and nails to fix the hidden track in place. You want to avoid any sinuous deflections over time if possible.
All that aside, there will come a time when you forget that you left some passenger cars in one of the tunnels, maybe a whole train, and you will run another train into the tunnel at speed. Something'll give, and that usually means lateral displacement of at least one item...and probably some damage if you run your trains at unrealistically fast scale speed. If you don't want a screw-off mountain top, your only other two choices are a side panel out of sight, probably behind the visible bench, or a duck under, crane your neck to see what you are looking for, and reach up and feel gingerly for the one or two items that will have to be pulled out and reset on the rails out in the open. The engines, unless you are on a steep grade, will pull the rest out of the tunnel for you once the badly derailed and hooked items are cleared.
One other tip. If your hidden track will be elevated extensively, either off the main framing or well above the floor, the next available "stop" on the trip with gravity, make a fence along the roadbed to corral the train that derials and wants to fall off. It was my solution. I had some left over spline roadbed leaf lengths, and just made some vertical posts along the right of way and screwed one length of the MDF spline to the posts, thus providing a safeguard for my expensive locomotives.
-Crandell