B doesn't have standing because they are indirectly harmed? So if I sell a home in an HOA without the HOA covenant on the deed, can the HOA sue? It seems they are also only indirectly harmed.

No because the HOA represents the other members of the community who were also subject to the same CCRs.

My understanding is that the HOA could sue you, presuming that they baked into your purchase contract the force of their authority.

You would then have violated your contract with the HOA.

I also expect that the city violated their contract with A('s heirs). B still has no standing.