[Python] Update PyO3 from 0.27.2 to 0.28.2

[dbrattli]

Summary

• Update PyO3 dependency from 0.27.2 to 0.28.2
• Add from_py_object to all #[pyclass] types that derive Clone (new PyO3 0.28 requirement)
• Replace deprecated Py::from_borrowed_ptr with Bound::from_borrowed_ptr + cast_into_unchecked

[github-actions]

Python Type Checking Results (Pyright)

Metric	Value
Total errors	18
Files with errors	4
Excluded files	4
New errors	✅ No

Excluded files with errors (4 files)

These files have known type errors and are excluded from CI. Remove from pyrightconfig.ci.json as errors are fixed.

File	Errors	Status
temp/tests/Python/test_applicative.py	12	Excluded
temp/tests/Python/test_hash_set.py	3	Excluded
temp/tests/Python/test_nested_and_recursive_pattern.py	2	Excluded
temp/tests/Python/fable_modules/thoth_json_python/encode.py	1	Excluded