After a lot of research and thinking and thinking again. I have figured out a logical theory on Beorn's background and the Beornings skin changing and history.
So, my take on the matter is that when Morgoth rose the Misties out of the ground to prevent travel a very small house of the Edain, let's name them House of Jeff, was living near or at the place where the Misties rose. It's likely most of the House of Jeff died from the rising of the mountains but the few who remain might've been affected by the Magic sort of like Nuclear radiation. This may have led to the Skin-changing abilities of the Beorn and possibly the House of Jeff.
Now let's fast forward a couple hundred years to the beginning of the 2nd age. The House of Jeff has grown attached to the Misties just the Beornings do to the Anduin in the 3rd age. The House of Jeff even feels as though are they part of the misties. But times are changing in the Mountains, Khazad-Dum is founded. This may be why the Beornings dislike the Dwarves since the dwarves are damaging the misties the House of Jeff dislikes them, however they wouldn't go to war over this they are too small and their cause injust. So the House of Jeff still lives in secret hidden from even the most prying of eyes. But soon a problem arises, the Goblins come. And since the House of Jeff was probably situated on top of where Goblin town now is the Goblins probably destroyed and demolished their homes. So the few remaining members of the House of Jeff (Now probably like 10-20 members) led by Beorn now leave for the Anduin.
It's now near the end of the 2nd age. The House of Jeff is gone despite it's prosperous life in the Misties. No longer does the House of Jeff exist their few surviving members are now the Beornings. The newly formed Beornings help each other build homesteads on which their families may live. However all of them are still in contact but don't make their presence known for fear of Sauron's strength. They live here in their farms for a good number of years until the 3rd age. Sauron is defeated for now and the ring is lost. Gondor grows in power and starts conquering Rhovanion. The Beornings hear of the new power but still don't reveal themselves as they wish to stay independent. But their seclusion is becoming ever so hard because of the growing number of people. Now probably measuring 1-2 hundred. After a bit Gondor recedes back to Minas Tirith. Some time later Bilbo and the Company arrive at Beorn's House. They finish their quest and Beorn invites them over for Yule. After the celebration the company leaves and the Beornings decide it's time to reveal themselves to the world, not only because it is becoming ever so hard to hide their growing population but also because they are done hiding. Beorn starts gathering the scattered men of the Vale and becomes Chieftain of the new Beornings. After so many generations the Old Blood of House Jeff runs in very fewer and fewer people. Now the numbers of Beornings measures 2,000 of them only 100 can skin-change.
Thanks for reading my speculation regarding the origins of Beorn and his followers! I hope you enjoyed it.