This one applies to every language. I was working with a python package that decided that, since `sys.argv` was available from anywhere, it should parse `sys.argv` to configure its own behavior. For a long time, their suggestion was to first parse `sys.argv` yourself, then to modify it before going into the library.
It was so ridiculous, someone ended up sending in a patch for the kernel to modify the command line once it had been parsed to remove the debug parameter.
Where flags shine is when you've some obscure tunable deep in the dependency tree that you need to tweak (particularly in an emergency). Plumbing through potentially thousands of flags through to main is nonsensical in that scenario.
Maybe you've seen a better flags library than I have, though.
When that came up what you'd do then is refactor that to be a class parameter or config option or whatever (and we'd usually ask that the flag be kept in some form).
Until then though you get the benefits of a quick and easy way to both expose and use tunables, which is much better than not having it at all.