src: remove `MarkIndependent()` calls
The method has been deprecated in upstream V8, with messaging indicating that it is the default for handles to be independent now anyway.
Refs: https://github.com/v8/v8/commit/71ad48fb8f214e80518ba0419796e4c571351255
Checklist
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make -j4 test
(UNIX), orvcbuild test
(Windows) passes -
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