Yes, sure would be nice. Bonus points for transparently pointing out what systemd changes onionjuggler is applying (where, what kind of changes).
I don’t think there is any convention in Debian or elsewhere how applications that create configs for users should operate as per configuration file location such as in /etc or /var and naming.
45_onionjuggler.conf looks good.
Not sure about the numbering:
config files numbering convention