lib: flag to conditionally modify proto on deprecate

[RafaelGSS]

Refs: #58218

In this specific benchmark, the performance difference between modifyPrototype=0 and modifyPrototype=1 is marginally significant at the 5% level:

• Mean (modifyPrototype=0): 390,196.99 ops/sec
• Mean (modifyPrototype=1): 382,521.21 ops/sec
• p-value: 0.05087

While this case is borderline, other benchmarks (e.g., #58907) have shown a more noticeable improvement, so I think this worth the change.

[nodejs-github-bot]

Review requested:

• @nodejs/performance

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 90.07%. Comparing base (a7a37c3) to head (b782bc8).
Report is 28 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main   #58928      +/-   ##
==========================================
- Coverage   90.11%   90.07%   -0.04%     
==========================================
  Files         640      640              
  Lines      188427   188466      +39     
  Branches    36956    36969      +13     
==========================================
- Hits       169792   169765      -27     
- Misses      11348    11426      +78     
+ Partials     7287     7275      -12     

Files with missing lines	Coverage Δ
lib/internal/util.js	96.16% <100.00%> (-0.68%)	⬇️

... and 34 files with indirect coverage changes

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[nodejs-github-bot]

CI: https://ci.nodejs.org/job/node-test-pull-request/67786/

[nodejs-github-bot]

CI: https://ci.nodejs.org/job/node-test-pull-request/67789/

[nodejs-github-bot]

CI: https://ci.nodejs.org/job/node-test-pull-request/67792/

[nodejs-github-bot]

CI: https://ci.nodejs.org/job/node-test-pull-request/67827/