I will try to answer your question from a Biblical perspective; it is quite complicated but I will try to streamline it.
The Indigenous people: After reading several translations of the Christian Bible and studying the Pentateuch extensively with Strong’s Concordance, I believe there were two Creations. The first being Genesis 1: 27, where man and woman were both created and sent forth to eat the plants and roam the earth and ‘multiply’ on the face of the earth. It is my understanding that these humans became the indigenous peoples and developed their own spirituality and religious rituals. Joseph Campbell’s ‘The Power of Myth’ gives a very well written and plausible explanation of how this could have happened.
The Muslim religion was ‘founded’ by Ishmael, the son of Abraham and Hagar (servant to Sara, Abraham’s wife, who was barren). After Sara bore a son for Abraham, named Isaac, Sara became jealous because Ishmael was Abraham’s first born and entitled to all inheritance, she insisted Ishmael be cast out into the wilderness to die. There was Divine intervention to save Ishmael and create a great nation (Genesis 17: 20). Ishmael and Abraham were descendents of Adam.
The Christian religion is a bit more complicated to explain partly because there is more known about it. It is my understanding that the Creation of Man (Adam) was an experiment that went terribly wrong. The perfect scenario of Man being caretaker of all life on earth was sabotaged by another sentient being (the Serpent). The Pentateuch (first five books of the Bible), in my opinion, is a parting gift, given as an explanation of what happened, what went wrong and what was done to try to remedy the situation to no avail. One of these attempts was with Jacob whose name was changed to Israel (Gen 32:28). Israel is the Forefather of all of the Hebrews of the Bible, later known as the Jewish people. After many, many attempts to rectify the situation, the Pentateuch was dictated to Moses and the effort was abandoned. Then Jesus Christ came into the picture who offered all of mankind the same ‘chosen, saved’ status with no where near the restrictions that the Hebrews had. Jacob (Israel) was a descendent of Adam.
I think you are asking about the geneology of these religions? Read the Bible or Google Ismael and Isaic two brothers from Abraham and Sara. This is were it all began, the same war we are fighting today. Ismael god said would be a "wild donkey of a man, always fighting with his brothers" The quaran holds Ismael as a important prophet and Mohammed a direct descendant, while the Jewish people hold Isaiac as the direct blessed descendant of Abraham. Side note the Bible unlike the quaran does show a complete geneology leading up to Jesus Christ.
This question...makes no sense. Islam isn't an "indigenous" religion, it's only ~1400 years old. As a result, anybody who worships an older faith (Bhuddist, Christian, Jew) could consider it a cult.
Also, even Christianity only started after 300 AD or so, with the canonization of the Bible in Rome.
So you don't have outside of a very small area, indigenous Christians...it's too new.
Perhaps you can add some more detail?