Align EoMT-DINOv3 modular classes with base segmentation implementation

[NielsRogge]

Summary

• allow the base EoMT layer and universal segmentation module to work with optional rotary position embeddings
• refactor the EoMT-DINOv3 embeddings and segmentation head to reuse the shared EoMT implementation
• refresh the DINOv3 configuration docstring formatting to match the updated signature

Testing

• make fixup (fails: interrupted after long repository checks in local environment)

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https://chatgpt.com/codex/tasks/task_b_68e611e4322483369d783331ee3237b4

[github-actions]

[For maintainers] Suggested jobs to run (before merge)

run-slow: eomt, eomt_dinov3