How to merge closely standing meshes using trimesh?

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Can I merge some non-intersecting but closely standing meshes? The only way I can imagine is just subdivide mesh many times and merge vertices by distance. Of course it's a horrible idea, but there is nothing else. Maybe I can turn geometry into some kind of metaball, which can keep original form but also merge with closely standing meshes.

Here is an example of what I'm talking about.

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