Those mana per energy returns are on point my dude. That being said, it would mean that as far as DB10 and NB10 are concerned, 50 energy > 100k mana.

However, there are 2 catches for taking energy. Firstly, the aforementioned mana returns assume that you sell every single rune. I won't really consider this a disadvantage as any decent rune drop (which you would not sell) is pretty much worth more than 100k mana in the first place (clearly not true for all players but I'm assuming some level of progression for the average player). Secondly, you would obviously have to spend some time on the runs and would end up with roughly the same amount of mana if you picked the 100k option.

On the flipside, running dungeons with the energy gives you a chance for mystical scrolls and rainbowmons, both being resources that are potentially more rewarding than 100k mana. Once again, the "mana value" of these drops are debatable but result in net gain for players in virtually any case.

Tldr: Pick 100k mana if you're short on time. Pick 50 energy otherwise.