I think you are confusing two entirely different locations. Logan Hill is on the Orin line in Wyoming.

I think the tunnel you are referencing in Nebraska is the one that was at the crest of Crawford Hill. Crawford Hill was and remains double track. That tunnel actually ceased to be a "railroad" tunnel when the main line was re-aligned (into an open cut) a number of years ago and the track was removed from the tunnel. The tunnel was only used for access to a maintenance road after that.

This is actually not the first time that Logan Hill has had four main tracks. See my photo from 1997:

http://www.robl.w1.com/Pix-3/I-971364.htm

This was during a rebuild of the line to alter the track spacing. BNSF has been trying, where possible, to have all new multi-track lines with 25-foot center spacing. That is the standard for still allowing maintenance work on one track without impacting the adjoining track. The long-time standard for multiple track had been 15-foot from center of track to center of track -- which did require, for safety reasons, adjoining tracks to be taken out of service during maintenance work.

As the 1997 rebuilding of Logan Hill was to get 25-foot centers, I assume that the new fourth track also has that spacing. Though there is a cut atop Logan Hill, this line is basically in open terrain, so there should not have been a problem getting adequate space (other than buying the necessary land).

-- Ernest