Refactor tolerance checking approach and tweak yaml configs

[lintool]

• Wrapped up Get rid of extra options for HNSW indexes #2531 - revert to "default settings" for dense indexing - previously was applied for some configs, but not others. This PR makes indexing options consistent across all configs.
• Tolerance values are now stored directly in the yaml configs, not centralized in run_regression.py
• Changed MS MARCO v1 passage Cohere regressions to use same metrics as other regressions.
• Updated topics - removed extra queries for BGE BEIR BioASQ

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 65.56%. Comparing base (204bc87) to head (a8ae8f9).

Additional details and impacted files

@@            Coverage Diff            @@
##             master    #2592   +/-   ##
=========================================
  Coverage     65.56%   65.56%           
  Complexity     1479     1479           
=========================================
  Files           225      225           
  Lines         13012    13012           
  Branches       1551     1551           
=========================================
  Hits           8531     8531           
  Misses         3953     3953           
  Partials        528      528           

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