I think a problem like this is better solved by making as good a model
as you can of the way the real-life object is constructed,
not by taking some mathematical abstraction.
The elevation of most points in a tunnel follows the elevation of a
line painted down the center of the roadway within that tunnel.
(This could be a fictional line, though in many cases an actual line
is conveniently painted there.)
On either side of the line the surface is at approximately the same elevation, but you may find the elevation increases or decreases
as you travel along the line.
If there are more than two access points to the tunnel (one at each end),
the additional access points are typically made via ramps that branch
off from the main tunnel and then travel some distance until they finally
emerge at the surface of the Earth. Each ramp can have its own slope independently of any other part of the tunnel.
If the given elevation of an "access point" is the elevation where the ramp emerges onto the surface, that elevation may not be the same as any nearby part of the tunnel.
As long as the ramps at the access points are not very long, however, they are likely to be at elevations that are not too different from the elevations of the nearby points along the main roadway of the tunnel.
They might be a few meters higher, but not hundreds of meters higher.
I believe the people who design tunnels generally do not care whether the center line of the tunnel lies all in one plane. They do care about the grade within the tunnel, that is, the slope of the center line.
A reasonable model for a typical tunnel through a mountain with two access points is that the grade is constant throughout the tunnel.
If the tunnel curves left or right at some point, it will more likely follow
a helical path there, not a planar curve.
So the first thing I would do in modeling elevations within the tunnel
is to "straighten out" your model of the tunnel to turn it into a
two-dimensional problem instead of a three-dimensional one; but the
two dimensions are not latitude and longitude, rather they are
elevation and driving distance through the tunnel.
For example, if the access points at the two extreme ends of the tunnel are $9$ km apart, but the driving distance between these points is
$10$ km because of the way the tunnel turns left or right,
lay out a straight line segment on the $x$ axis of a graph
with one end of the segment at zero and the other at $10$ km,
and plot the elevations in the $y$ direction.
Plot every other access point at the $x$ coordinate that represents the
driving distance from the "zero" end of the tunnel to that access point.
Provided that the ramps are very short compared to the length of the whole tunnel, a reasonable first approximation is that if there is an access
point at distance $x$ with elevation $y$, the elevation of the
main tunnel at distance $x$ is $y$.
Between access points, a reasonable first approximation is that the
grade is constant.
In other words, if you have $n+2$ access points (the two ends and $n$
intermediate access points) then the graph of the tunnel's elevation
consists of $n+1$ straight line segments linearly interpolated between
consecutive points among the $n+2$ plotted elevations of the access points.
You could make further refinements to the model given real-world knowledge
of how tunnels are built.
For example, you might observe that an intermediate access point is
far above the straight-line path between the elevations of the
access points immediately before and after it, the tunnel engineers
will typically let the main roadway pass a few meters below the access point
and make up the difference by increasing the grade of the ramp to the access point. (I don't know for a fact that it works this way; this is something you would have to get from real-world observations or from tunnel engineers themselves, either directly or via someone else who obtained that information.)
You might be able to refine the estimated elevations by finding out
which directions of traffic in the tunnel have access to each access point.
For example, an access point to an east-west tunnel that allows drivers
to enter the tunnel in the westbound direction is likely to merge into the
main roadway a few dozen meters west of the access point. You could estimate where that point was and plot the access point's elevation at the $x$ coordinate of the merge point rather than the $x$ coordinate of the
point in the tunnel closest to the access point.
Another real-life observation is that when a tunnel crosses a river, its elevation is often lower in the middle than at any of the access points,
because the tunnel is designed to pass below the bottom of the river.
But I think all these extra refinements would only change the estimated
elevation of the tunnel's roadway by a few meters at any given point.
The main source of error that you're trying to correct, following the
surface elevation rather than following a reasonable grade for a tunnel,
is corrected by a very simple 2-D linear interpolation.
The main thing to "correct" after that would occur when tunnels pass
under rivers, and for that you may just have to make a reasonable guess
(e.g., put the tunnel $100$ meters under the surface of the middle $1/3$ of the river, if that is below all the access points, and let it slope upward from there).