[python] Update Scene create method in the Python API

[jp-dark]

1. Add spatial disclaimer as warning.
2. Implement writing the coordinate space at create.
3. Use Scene C++ code instead of going through Python superclass.
   • 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 85.92%. Comparing base (b6af5d7) to head (84c72ae).
Report is 20 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3356      +/-   ##
==========================================
+ Coverage   85.65%   85.92%   +0.27%     
==========================================
  Files          57       55       -2     
  Lines        6203     6189      -14     
==========================================
+ Hits         5313     5318       +5     
+ Misses        890      871      -19     

Flag	Coverage Δ
python	85.92% <88.88%> (+0.27%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Components	Coverage Δ
python_api	85.92% <88.88%> (+0.27%)	⬆️
libtiledbsoma	∅ <ø> (∅)