Ah hah. Sorry, I did misunderstand what you are referring to.
Yes, the naming of the menu in Meshmixer is indeed is very unfortunate, particularly for people that work a cross applications such as Fusion 360 and Meshmixer.
In the 3D world you are not dealing with one industry but two very distinctly different industries that use 3D software for a different purpose.
1. The purpose of CAD software is to create models for manufacturing. That drives the need for the mathematical precision described in my last post and informs how many of the modeling tools and workflows in CAD software are designed. This is mostly the world of BRep and NURBS surface models. This is also the industry that developed the .stl format so designs could be 3D printed.
2. In the beginning models for 3D computer graphics and animation were also created using NURBs surfaces, bot those proved to be difficult to handle and as such polygon and Sub-D mesh modeling software such as Maya and Blender were developed. The purpose of these software packages was to create models mostly for visual representation computer graphics and animation. Here mathematical precision is less of a concern and we are working with meshes that consist mostly of quad faces. Nowadays they are also often used for industrial design and product design.
Both of these industries use triangulated meshes nowadays mostly available in .stl or.obj format, but again mostly for a different purpose. In CAD the sources are often 3D scans with the intention to reverse engineer the original geometry.
Polygon and Sub-D modeling software creates these with sculpting tools.
BTW that is not the Sculpting in Fusion 360, another real unfortunate name, which is really Sub-D mesh modeling and not real sculpting in say ZBrush).
Then there are of course sites like thingyverse where people can stare .stl files created in either software category purely meant for 3D printing these objects. However often enough folks want to modify these .stl files and that can be difficult.
Your landscape mesh falls more into the scan area. The online tool you used scans a 3D data set in and create a mesh form it, which is very uniform in structure, with very evenly sized triangles, which helps creating bette geometry for your purpose. It is so uniform and grid-like that in fact I believe it would be possible to re-write this so it can create a quad-mesh directly.
Once you have that mesh, the question is: What do you want to do with it.
If you only wanted to 3D print it tun could likely send it directly to a 3D printer/slicing software.
As I understand it, you want to remove a particular potion of it ?
For me that is still exactly clear what modifications you want to do and what the best approach is to actually do it.
Do you want to cut off a section to remove part of the terrain you are not interested in - this would obviously alter the rectangular/box shape of the object, or do you want to maintain the rectangular shape and just flatten a particular part of the terrain to blend in with it's surroundings.
The next question to answer is what do you want to do with the object or bore specifically, if you want to "make" it, by what means. You've already answered this, but I'll go over this anyway.
You can directly machine .stl files in Fusion 360's CAM package, but I don't have experience in that area. Maybe @LibertyMachine or @HughesTooling can answer that.
However, a mesh is a mesh and it will retain its faceted nature. If the mesh resolution is relatively coarse and depending on the method of manufacture this can be seen in the end product and often that is not desirable. Thus we'd want to smooth the mesh. This is done by re-meshing a (semi) automated form of re-topologizing the triangulated mesh into a mesh consisting only of 4-sided polygons. The key task is really yo re-create topology.
That's what I used InstantMeshes for. There are other a number of tools that can do this, but not all of them are available for free.
Once we have that quad-mesh, then we can still decide to work with it in a Sub-D modeling application egg, Maya or Blender, but I won't go into detail here why that may make sense. Or we can use that quad mesh to get to. NURBS surface. NURBS surfaces and Sub-D surfaces share some mathematical similarities.
In case of Fusion 360 the intermediary step between and an imported quad mesh and a NURBS surface is a T-Spline.
As discussed already we end up with a NURBS surface, a mathematically precise description hopefully close enough to the original mesh.
The surface and in the case of the solid model I showed in a post above can then be machined in the CAM environment.
While this is not widely known it is not "arcane" knowledge by any stretch of the imagination. There is nothing secret, or mysterious about it and it can be easily found on the internet if you know the proper terminology and are able to connect the dots between new different technologies and methods. There are plenty of detailed research papers such as the one published on the project page for InstantMeshes.
However, your project resides more on side of the CAD industry and quite frankly, the majority off CAD users are fairly uninformed about such topics. They have gotten so used to things just working out that they've stopped understanding sometimes of even the most basic underlying principles of the tools they are working with. People that use Sub-D molding tools are generally much better informed about the underlying technologies used in their tools than the usual CAD hobbyist and many professionals and as such there is not much information about it in the CAD sphere.
