test: relax tolerances and remove flaky index-on-disk assertions

[eguguchkin]

• I have read and followed all requirements in CONTRIBUTING.md;
• I used LLM/AI assistance to make this pull request;

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 70.45%. Comparing base (f895e5f) to head (e92ce44).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #455      +/-   ##
==========================================
- Coverage   70.48%   70.45%   -0.04%     
==========================================
  Files         232      232              
  Lines       18346    18346              
==========================================
- Hits        12932    12926       -6     
- Misses       4441     4446       +5     
- Partials      973      974       +1     

☔ View full report in Codecov by Harness.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
• 📦 JS Bundle Analysis: Save yourself from yourself by tracking and limiting bundle sizes in JS merges.