Reducing faces and vertices in user generated models

Outline:

I am making a simple building game that will allow players to create custom prefabs from primitives, then build them in game. The aim is to allow mesh deforms etc so the basic unity block prefab is not up to this task, nor the unity plane.

Here is a common scenario that I am trying to solve, with the current process and 2 ideas I have had for potential solutions. I need advice on whether the solutions are possible/feasible and if either would be better. Some advice on where to focus my attention for learning more about this is subject in detail would also be much appreciated.

Scenario:

I have 15 4.5k blocks arranged as a 5x3 wall. I make some dents and protrusions through mesh deforms in some of these blocks, and now want to export them.

Current Process:

1 - Check wall for any blocks that have not been edited.
2 - Replace unedited blocks with default unity cube mesh. 3 - Combine Mesh. 4 - Export Obj.

Problem:

Exported model has a potential for a large number of hidden tris, which are still processed:

If a modification was performed on each block in the wall, I could potentially have 33k hidden tris, out of a total model count of 60k That is something that has to be resolved.

Potential Solutions:

1 - Find out a way to locate all the hidden faces and their relevant vertices, and remove them.

2 - Find out how to create a plane for each face of the mesh from the combined mesh, and combine as a new mesh.

Are either of these realistically possible, or should I be looking in some other direction completely? If either of them are realistically possible, where would I go to get some more in-depth information on manipulating meshes and vertices etc from, for someone who needs to learn a whole lot about this subject.