Hmm - honey in marmalade is not something I have done or heard about - I am wondering if the heat might change the honey either in flavour, or its enzymes - honey is actually well, not alive, but active, in a way.

If you buy the clear, runny honey and leave it, it reverts back to the opaque stiff form eventually. It has not 'gone off' it is just what honey does.

Personally I would keep things simple and if you want to mix the flavours just put two jars on the table. It would be a shame to lose both the marmalade and the honey if there was some riotous reaction in the jar, or if the process was not successful in some other way.