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GH-40227: [R] ensure executable files in `create_package_with_all_dependencies` (#40232)

### What changes are included in this PR?

-  Set the `utils::tar` `extra_flags` argument to `NULL` (default `""`). This benefits from logic baked in (also used by `R CMD BUILD`) that checks the mode of `configure` and `cleanup` files and sets them to be executable if they are not already.

### Are these changes tested?

No. I didn't see any existing tests for this function (which perhaps is not a valid reason). 

### Are there any user-facing changes?

No. Although if `configure` and/or `cleanup` are not executable, that will be corrected with a user-facing `warning`.

* GitHub Issue: #40227

edit: revised the description based on the new approach in 40e8add.

Authored-by: Paul Donnelly <donnelpa@gmail.com>
Signed-off-by: Nic Crane <thisisnic@gmail.com>