Or they just need freaking powerful sealing jutsu and be insanely adept with using them, if you can seal Kaguya, you can seal Naruto, Sasuke e and co.
I don't think we would hear about new kinds of power sources, at least not until very late in the story's development. The mark in Boruto disrupts chakra, and given the recurrent theme that the Ootsutsuki somehow are adept (or maybe even dependant) on consuming chakra and natural energy, the seals are probably related to that than to new kind of energy. If you really want to end the shinobi world you'll have to revert mankind to the time prior to Hogoromo´s teachings, where people didn't have the ability to access spiritual energy, the best way to achieve this is to lock chakra away somewhere it can't be accessed, just like in the beginning all chakra was stored in the Shinju, the easiest way would be storing chakra on another dimension in which you'll can't access without chakra.
The flaw in the whole concept of Shinjutsu as another source of power in the form of "spiritual energy" is that chakra already is the mix of physical (shintai) and spiritual (seishin) energies, and spiritual energy is already an almost infinite source of energy since it can be expanded indefinitely by study, meditation and experience. Chakra (the mix of spiritual and physical energies) is only limited by the physical condition/stamina of the user. There are people like the Uzumaki clan which have a body with a higher ability to develop their own physical energies, thus allowing them to access more spiritual energy and people like Orochimaru or Kakashi with a more limited ability to develop their own physical energy, just like there are people in real world which physical constitution allow them to develop more muscle mass than other or people with a body type that allows them to run very fast in very short time and other which can run for very long times albeit not so fast.
Since the whole concept of a spiritual based energy already exists it is unlikely that something similar will show up, at least in the form you described. But there's always the possibility of something on those lines.
Also the problem with using natural energy is not that very few people are able to tap it or that thet die or go crazy simply by tapping it, the real problem is that it is very difficult to balance. Fukasaku's explanation to Naruto still holds, essentially when you tap natural energy you instantly access the total energy of the entire world around you, and it need a lot of physical energy to be able to access the large amount of spiritual energy needed to balance the three kinds of energy, since most people don't have enough physical energy to do so they can't use it, and even when they do, very few people have enough control over the 3 kinds of energy needed to balance it for prolonged time. It is like an amateur pool swimmer being thrown into the surf on a very windy and stormy day, despite their ability to swim very well, very few would survive for long times because very few have the stamina to withstand it. Juugo's clan goes crazy with natural energy exactly because they can't balance it well enough and start to transform in whatever weird beast natural energy transforms people before they become stone.