Both Git and Emacs are highly customizable. Magit is both a Git porcelain as well as an Emacs package, so it makes sense to customize it using both Git variables as well as Emacs options. However this flexibility doesn’t come without problems, including but not limited to the following.
When a certain Git setting breaks Magit but you want to keep using
that setting on the command line, then that can be accomplished by
overriding the value for Magit only by appending something like
("-c" "some.variable=compatible-value") to
magit-git-global-arguments.
fetch.prune=true are respected by Magit
commands (because they simply call the respective Git command) but
their value is not reflected in the respective transient buffers.
In this case the --prune argument in magit-fetch might be active or
inactive, but that doesn’t keep the Git variable from being honored
by the suffix commands anyway. So pruning might happen despite the
--prune arguments being displayed in a way that seems to indicate
that no pruning will happen.
I intend to address these and similar issues in a future release.