I don't think so. What you are saying is true if for some reason you want to work with absolute values, but nobody would do that. You measure many data points as your submarine flies over the landscape for a time, and then you match the measured curve with predicted curves from bathymetric maps. This is an optimisation problem where you try to find the best match. Precise elevation is an output from this process not an input requirement.
> but when things don't vary much (i.e flat topography and not a ton varying geologically), you don't have much of a unique signal to match to
100%. This is also true for cruise missiles which fly by TERCOM[1]. And there is an interesting consequence to it. Submarines and cruise missiles don't just bumble around randomly. The navigators also know this limitation so they set trajectories which plays to their strength. In the case of the cruise missile planners they have tools to evaluate the navigational quality of a terrain contour matching algorithm over a proposed trajectory with Monte Carlo methods. Probably submariners have the same.
This means in practice you can know that the submarines are more likely to take certain routes. They will prefer approaching from hilly terrain over flat, but also over extended flat areas they will prefer to overfly butes to regain navigational accuracy. This of course won't tell you precisely where the submarine is, but can help an adversary more economically allocate their ASW assets.
> At any rate, it's a very useful tool for many other things, but I'm skeptical it could be turned into a precise navigational aid
Yeah. I mean I heard that people proposed to make measurements of stars to find your location. The fools. Haven't they heard of clouds? Sometimes you can't see as far as your own nose for days.
Every navigational system ever devised have limitations and peculiarities. If you are comparing gravitational tercom with the ease and quality and simplicity of GPS then of course it will look crude and cumbersome. But of course GPS adds other complications and dangers to the life of a submariner. Used well, and in the right circumstances it can be potentially very valuable technique.