[REFACTOR] Optimize dual contouring vertex generation and add vertex overlap configuration

[Leguark]

Optimize Dual Contouring Vertex Generation and Add Configuration Flag

This PR introduces several optimizations to the dual contouring vertex generation process:

• Adds a new DUAL_CONTOURING_VERTEX_OVERLAP configuration flag to control vertex overlap behavior
• Refactors the vertex generation code with significant performance optimizations:
  • Eliminates redundant memory copies and intermediate arrays
  • Improves matrix multiplication efficiency with backend-specific optimizations
  • Enhances voxel filtering logic to only process valid voxels
  • Optimizes mass point calculation with more efficient algorithms
• Simplifies function interfaces by merging _generate_vertices into generate_dual_contouring_vertices
• Improves vertex overlap handling with better parameter naming and conditional execution
• Updates overlap logging to show only relevant keys instead of full data structures

These changes maintain compatibility while improving performance and code clarity in the dual contouring implementation.

[Leguark]

• [REFACTOR] Optimize dual contouring vertex generation and add vertex overlap configuration #36 👈 (View in Graphite)
• [ENH] Implement surface-based dual contouring with optimized triangulation #35
• [REFACTOR] Modularize triangulation code with helper functions for improved readability | GEN-13490 #34
• [REFACTOR] Optimize dual contouring gradient handling and normal correction | GEN-13490 #33
• [FIX] Correct vertex index calculation in meshes_to_subsurface method | GEN-13490 #32
• main

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