To me, the fact that duplicati does not set the bit itself is actually an advantage, because that way I know that I’m in complete control of that bit and can hence use it for the indicated purpose. In other words, my suggestion is to use the archive bit in quite a different way that it was originally intended. And I think it is possible to do this, because it is rarely been used anymore. A bit like when they decided to use the @ symbol for emails because it wasn’t used for anything else.
Yes, there is a risk that other programs might still use it and duplicati should perhaps warn about this in the help text, and perhaps it should not be in the GUI at all, but as a commandline/text option, I think it should be okay.