Deep copy PipelineOptions and keep the input intact.

[shunping]

Users typically expect the pipeline options they provide to remain unchanged after running a pipeline. Therefore, we make a deep copy of the provided options to prevent any accidental modification or "overwrite" during pipeline preparation and execution.

fixes #34722

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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 56.48%. Comparing base (8cd0a29) to head (bd46c97).
Report is 7 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##             master   #34723    +/-   ##
==========================================
  Coverage     56.48%   56.48%            
  Complexity     3289     3289            
==========================================
  Files          1178     1179     +1     
  Lines        180978   181164   +186     
  Branches       3399     3399            
==========================================
+ Hits         102220   102327   +107     
- Misses        75499    75578    +79     
  Partials       3259     3259            

Flag	Coverage Δ
python	81.25% <100.00%> (-0.07%)	⬇️

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