[python] Update Scene create method in the Python API

[jp-dark]

1. Add spatial disclaimer as warning.
2. Implement writing the coordinate sapce at create.
3. Use Scene C++ code instead of going through Python super class.
   • Requires updating Scene C++ create method to match behavior of existing code (do not create obsl/varl/img at create).

[jp-dark]

sc-58718

[codecov]

Codecov Report

Attention: Patch coverage is 88.88889% with 2 lines in your changes missing coverage. Please review.

Project coverage is 85.77%. Comparing base (b6af5d7) to head (63cf516).
Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3356      +/-   ##
==========================================
+ Coverage   85.65%   85.77%   +0.12%     
==========================================
  Files          57       57              
  Lines        6203     6216      +13     
==========================================
+ Hits         5313     5332      +19     
+ Misses        890      884       -6     

Flag	Coverage Δ
python	85.77% <88.88%> (+0.12%)	⬆️

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Components	Coverage Δ
python_api	85.77% <88.88%> (+0.12%)	⬆️
libtiledbsoma	∅ <ø> (∅)

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