What we need are real world empty weights for the two versions, since variations in assumptions about configurations can produce very different payloads in the simplified, if not simplistic, one page executive summaries and sales brochures.
It makes no sense for a converted airframe, with a lower MTOW, to have a higher payload. None. Besides the previously mentioned remnants of passenger windows and exit doors, common sense tells us that Boeing would not add unnecessary weight when building freighters from scratch.
The nose door is the only weight penalty that pure freighter carries, and I am sure Boeing would be happy to build a 747F without it if a customer wanted it that way.
If there is a problem with the conversions it is probably optimistic/misunderstood empty weight estimates. Or to put it another way, too many MBAs and too little industry experience.