When I created a file ~/.config/inkscape/templates/default.svg, it was not used as the default template when I created a new document.
I has to rename it default.fr.svg, and then it worked (NB: my system has a french locale).
My understanding is that, if inkspace finds a *localized* default template, it overrides a non-localisezed one. Since /usr/share/template/default.fr.svg existed, this one overrode my personal default.svg.
I think a *personal* (i.e. in ~/.confifg) default.svg should override any *system* default*.svg.