In the basement of the house of Charles Randall (Adam's father), we can see the tree of life (as an optional thing to found)

https://vignette.wikia.nocookie.net/tales-from-the-tower/images/5/5d/VicarageTreeImage.png/revision/latest?cb=20090919152122

The tree of life seems to be located in Sheol, in the white tower (which is also optional). What is the meaning of all this? Why Charles Randall had that in his basement?

For me, the Vicarage is the strangest place in the entire game, stranger even than Sheol with its arcade-style puzzles. Judging by the beast caged in the basement, I think Charles Randall experimented with the supernatural. His living room is also odd for someone his age and stature.

And what's your opinion on the three lights in the Tree of Life? Perhaps they symbolize Adam and Rebecca (and someone else?) coming to save humanity?

Hm, that would be a stretch. Most likely it's just an effect added by the designers to show its mystical nature. Unfortunately, lot of questions from this game will remain unanswered. I cannot shake the feeling that they wanted to do more with the vicarage, but maybe didn't have the time.