Dear Brother,
I believe that this is exactly the main point that makes the difference. It is said that God is not omnipresent and he comes to establish the temple of Shiva where only one shivling is worshipped.
Omnipresence does not concern only physical stones, mud, cats and dogs that god is not in them, but also such souls with such stone like intellect that he wouls not come in them, souls that fight like cats or are lustful like dogs. He will still be coming in the one who is highest on high amongst the human beings, the first Human being Adam, who is firm in his faith and not like mould of mud that on a little kick of Maya would break away from the path of knowledge.
If he used to come in many then many speak different things that does not tally and contradict with each other. It is said that he is one and gives only one direction. If he still does service trough others, like said in the Murli, this is not to confuse us whether he is present in one or in many. He is present in one, then what service he does we don't know what he does. We may think when good service is done that it is he who has done still he has a fixed Chariot.
It is said in the bible that we should have only one God and no one else, then, if we think he comes in many we go to each one and say yes, whatever you say is true, it comes from God, yes whatever you say is true. Then how many Gods in corporeal form does it make? It makes many gods. With this practice the intellect becomes confused, listening to different things from different sources. It does not make a temple but a brothel, where the prostitude listens and obeys whoever comes to her. A faithful wife is faithful only to her husband. We are all souls like wives of one husband.