Config files introduce a whole slew of complexity: race conditions, a whole bunch of new error conditions (permission denied, parse errors, read-only filesystems, disk full, etc.); system- or user-wide config files are spooky action-at-a-distance, which can make problems hard to track down, makes commands non-deterministic and may impact reproducibility (e.g. on other people's machines).

If commands insist on taking options via a config file, my preferred way to call them is to generate the config in-place via process substitution, e.g.

    someCommand -c <(printf 'foo\n\tbar="%s"\n\tbaz="%s"\n' "$BAR" "$BAZ")

Although this isn't always possible, e.g. if 'someCommand' tries seeking around the config file rather than just parsing it in one pass.