Thanks, but actually I just meant the duplicates, not both sets.
However, since the purpose of these files is upstream auto-updates, and that conflicts with downstream package management anyway, then for the purpose of distro packaging these files should not be installed at all, since at best the result would be unmanaged files, and at worst we’d end up with broken dependencies.
Simply omitting those files will prevent that, however that leaves a non-functioning option in the UI, which in itself isn’t a serious issue, except that it might cause confusion and needless bug reports. The cleanest solution would be a build-time configure option to remove the auto-updates option in the UI, but in the meantime I can simply apply a patch for downstream use.