perhaps some explanation of intent would help.
the deb/rpm packages have entrypoints for weewx utilities at /usr/bin/wee*. these are shell scripts that invoke the actual weewx 'binaries' in /usr/share/weewx. there are two reasons for these: (1) they ensure that the weewx utilities are automatically in every user's path, and (2) they provide a mechanism for customizing/overriding the python implementation used to invoke weewx. customizing is done using /etc/default/weewx (i know, this probably should be /etc/sysconfig on redhat systems. sorry. and it is /etc/defaults/weewx on *bsd systems). the variables are WEEWX_PYTHON, WEEWX_BINDIR, WEEWX_BIN, and WEEWX_CFG.
the weewx-multi script is functionally one level up from that. it has a WEEWX_BINDIR that indicates where the weewx binaries are located, as well as WEEWX_INSTANCES, WEEWX_USER, WEEWX_CFGDIR, and WEEWX_RUNDIR variables. it will work with any type of weewx installation (setup.py, deb, rpm, etc), although it does currently have debian tendencies (all of the lsb stuff). the variables can be overridden in /etc/default/weewx-multi so that you do not have to modify the weewx-multi script itself.
finally, it is my intent to push the capabilities of weewx-multi into the 'standard' weewx init.d script, and make the package installers detect whether to deploy an rc script or a systemd unit file. that is complicated by the fact that (1) there are (were) different conventions for init scripts on redhat vs debian vs suse vs *bsd, and (2) we now have to keep systemd happy too, which means doing a variation of the weewx unit file that has weewx-multi capabilities (perhaps kinda like openvpn has done).
m