How to signal sole affiliation is honorary?
An honourary appointment at my university comes with an email address, library privileges, internet access and a hot desk. In exchange, we advise our honourary staff that we are happy for them to list their affiliation with us in two wways: (1) "Honourary Research Fellow" or (2) "Research Fellow (Honourary)". They are, of course, under no obligation to do so.

In the journals I help edit, affiliations listed as honourary or adjunct or visiting carries no stigma. We treat it like any other affiliation. However, because there is a cap in the number of affiliations authors can list (we allow no more than three), an honourary affiliations are included in those counts.

Good luck!