but I need to keep faces that are coincident at the areas that the meshes collides the same for each one (bottom faces of top mesh in the same spot as the top faces of the bottom mesh). I need them to have the same boundary faces and no gap so I can make some simulations at the fea software later.
You may be able to use explode to get the sides as individual meshes, then use MatchMeshEdge with RatchetMode=Off to match the meshes to each other. This works best if the deviations are small and the number of quads on both sides is the same.
I’ve managed to make this work (kinda) with rebuild mesh from pufferfish in grasshopper with the weld settings, the challenge is to split the full mesh into two separated meshes.
If your goal is FEA simulations you may be using the wrong tool to get your element mesh. I am not an experienced mesher, but I know tools like Gmsh, Salome and commercial grid generation packages are better suited to get meshes where quads on different parts need to be aligned. These also have much more options to finetune your mesh.