in recent versions of gpg 2.1, dirmngr is not generally intended to run as a
system-wide daemon. From dirmngr(8):
For historical reasons it is also possible to start dirmngr in a system daemon mode which uses a different directory layout. However, this mode is deprecated and may eventually be removed.
But gpgsm has the option --prefer-system-dirmngr, which is not explicitly marked
as deprecated (and on Windows it is always used):
--prefer-system-dirmngr If a system wide dirmngr is running in daemon mode, first try to connect to this one. Fallback to a pipe based server if this does not work. Under Windows this option is ignored because the system dirmngr is always used.
These seem to be in conflict with one another. It would be good to align them.