Hello, I'm a newcomer as a Devuan user.
I had a similar situation where /.config or /.cache were created in MX Linux as same as Devuan.
So I thought it might be an init issue since SysVinit is common.

After I read this thread, I took note of the pulseaudio home directory.
The user "pulse"'s home directory is /run/pulse, defined in /etc/passwd.

However, /run/pulse was not exist in my fresh installation.
Other similar daemon home directories are existing, e.g. /run/openntpd, /run/avahi-daemon, or /run/sshd.
grep mkdir /etc/init.d showed that these directories were explicitly mkdir'd, except /run/pulse.

Therefore, I have added an init script that does mkdir /run/pulse && chown pulse:pulse /run/pulse and it seems that /.config is no longer recreated now.
The files are not actually placed in /run/pulse even after I added it, but it may be origin for determining some relative directories.

I hope this will be of some hint.
Thanks.