My understanding is that Rafales will be considered only if MMRCA is won by them. Considering that this can be included in their overall contract to supply these additional 40 fighters, I think that MOD will not specifically ask for "40 nuclear capable fighters for SFC" since that will raise a lot of eyebrows in the international community and we'd be expecting a load of vocal garbage from neighbourhood about "destabilizing south asia". The 40 jets are mainly going to be something that IAF already or is planning to operate. Creating additional infrastructure for just 40 fighters will be crazy and needlessly costly which we want to avoid.
And if at all it is going to be something "slightly" different from the regular IAF fighters, I would seriously consider Su-35BMs. Those things are lethal, very similar to MKI therefore requiring less training, maintenance infrastructure needs slight changes only and BMs can carry more payload and more fuel compared to Rafale. Not to mention, they've AESA (from Russia's MiG-35 plan), state of the art weapons, 3D TVC and extended range. Mixing 40 single seater Su-35BMs with the 2 seater MKIs would be a great idea and since SFC and not IAF is managing this, it won't create much hassles.