sorry for double posting but the edit button seems to have been removed...so i cant edit, but anyway:
after reading chapter 67 again, i remembered that Dr Marcoh said that Amestrian alchemy utilises the enery from tectonic movement and other geological phenomena.
chapter 67, page 33:
Mei-Chan:it seems the alchemy of Amestris does not use Lung Mei.
Marcoh:Yes, we use the energy of the movement of the Earth's crust.
therefore, unless Father is channeling his power through the Earth in order to power the alchemic reactions of Amestris and using this to confuse alchemists (to what end I don't know),
Originally Posted by Cardboard Box Junkie
Homunculus, who at some stage changes his name to Father, travels west and teaches the people he meets an alchemy that taps into the power of the Souls of Xerxes Father has contained in his body, which becomes known as Renkinjutsu.
cannot be true.
Although, Mei-Chan later brings doubt to this 'use of the tectonic energies' theory, by saying:
"Rather than the fluctuations of the Earth's crust, this power that flows under our feet, it feels like a great number of people are squirming around"
Also, Father stopped all alchemy during his battle with Ed and Al (but to what extent we don't know).So there is a possibility that Father does control the fluctuation of energy in Amestris, however, it still seems unlikely, to say the least, that he is the one controlling all the reactions within Amestris.
One more thing just came to mind: when Father effectively stopped Ed and Al from using alchemy during their fight, perhaps he was just dispersing the energy like Ed did during his second fight with Scar.
So, in the end I guess we just don't know...but theories are pretty fun to waste time on though.