When comparing the costs, performance, energy requirements the additional limitations of CMOS are that you still mainly have fairly large chips that have to be put into fairly large form factor devices.
Rod-logic in a pure molecular manufactured systems would have far less size overhead.
Rod-logic can be three-dimensional which greatly increases its likely performance.
The amount of computing in a volume for CMOS, you can only make something so small if for CMOS you have to have the chip + power supplies + supporting logic chips + connections + packaging + cooling + substrates etc... the all in size (including overhead) and costs.
There is still the attempt at Ball semiconductor to make, spherical chips. Seems to have had very little progress over the last 5 years.
Multiple layered chips and reversible computing do not seem to be discussed in the roadmap.
Another separate thing is the hybrid NRAM memory. Nantero and LSI logic.. Those companies say they will have sample production this year and full scale production next year. A loop of nanotube for each silicon circuit to hold the charge..making DRAM nonvolatile.