clean more flags/args code from operator and removes redundant functions

[ChrisJBurns]

There were still some pieces of flag code lying around the code base as well as some supporting functions that were unused.

Ref: #2195

[codecov]

Codecov Report

❌ Patch coverage is 60.00000% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 54.28%. Comparing base (2642816) to head (ef45ee2).
⚠️ Report is 6 commits behind head on main.

Files with missing lines	Patch %	Lines
...md/thv-operator/controllers/mcpserver_runconfig.go	60.00%	1 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2343      +/-   ##
==========================================
+ Coverage   54.22%   54.28%   +0.05%     
==========================================
  Files         241      241              
  Lines       23602    23446     -156     
==========================================
- Hits        12798    12727      -71     
+ Misses       9592     9505      -87     
- Partials     1212     1214       +2     

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[jhrozek]

these really do look unused, great work trimming the fat