Istoleyourtaco
first off your correct it is 3 off and ofcoarse you would need to expend energy you would need to even if it was just 1 away no one said you didn't need to . They point of turning lead into gold is value yes but that doen't make them not equivalent in a natural way. second gold and lead are still equivalent both sre soft metals with similar structures, Also as you in your post in a molecular level it is not an upgrade as you like to say if anything it is a downgrade.Thrid I never said the philosophers stone is the only exception I said it was one exception. In the FMAB movie there was the milovians version of alchemy to. You also notice how the law of equivalent exchange is called the base of alchemy . You know what you do with a base you build on it and it changes.Take both FMA and FMAB both are very different but yet both are very similar. Both have a same kind base but both went in two different paths.
Turning it on it's head also means they're changing the base of the theory, which you can see from Alphonse's explanation of it. And no, they're not equivalent in a natural way. Both of them are soft metals, but they both have different uses and different properties. Removing or adding protons isn't really an upgrade or a downgrade, just a change. However, that inherently makes the two unequal because they are unequal weights, so on a molecular level you need to remove something.
But, yeah. Alchemy itself needed the power of souls to operate. That's why Armstries was a military state that was constantly at war. They needed the power of a lot of dead people to be able to turn the country into a philosopher's stone (which is what Father and the homonculus were up to). Xing used a different kind of alchemy, but that required them to need tools to draw energy from the ground (Mei's kunai with talisman).
However, the point is, there's a cost involved in both reality and fantasy, and the input doesn't always equal the output. Even look at human transmutation- the losing of limbs, your organs, whatever is penance... not equivalent exchange. What they got out of it was barely even human and not even the human they were trying to make.