I'm not sure to understand what you mean ... The new manager (v2) can't launch roms, that feature has been disable as far as I remember (@DjLeChuck can you confirm ?).
No, it's definitely not disabled, it's just broken, because the API is broken.
Now I've got the API working in 4.1 it will launch ROMS from within the V2 manager, but as @kjbstar pointed out, it fails to relaunch ES after the ROM is quit. I'm going to have a stab at fixing the way that the API handles ROM launching, because, as you point out, at the moment it's not performed by configgen.