No, adding 'createhome=no' stops it creating a home directory and is what I am currently using (in addition to system=yes) as a workaround to get the desired result.
I just tested and the home directory is created on the first run - on initial user creation.
I also tested manually running a 'useradd -r' to make sure it wasn't something funky with my OS build (vagrant box - lots stripped out) but that works as expected - no home directory.
If the command is supplying '-r' then it would seem a good call that something is overriding that somewhere and explicitly forcing the creation of a home directory. However it seems to happen on the first run for me, so unless that 'missing homedirs' check is executed on first run, somewhere else might need looking at too.