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message isn't a valid option under execute:, so Quarto ignores it.
At the document level, warning controls both warnings and messages, which is why warning: false hides your message.
The options you can set under execute: are listed in the documentation: https://quarto.org/docs/computations/execution-options.html#output-options

message is specific to knitr, and the Jupyter and Julia engines have no equivalent, so it isn't a shared execute: option.
#| message: false works on a single cell because knitr handles the cell options itself.
To set it for the whole document while you keep warnings, you can pass it to knitr directly:

---
title: "My Document"
format: html
knitr:
  opts_chunk:
    m…

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Answer selected by richardjtelford
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engines-knitr Anything regarding knitr engines computations
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