It is doubtfully a question of translation sources as the Masoretic Text (commonly abbreviated MT) supplies the base of almost all English translations from Hebrew. Other translations and versions will be examined, especially ancient ones, but translators going from Hebrew start with the MT. (Obviously a translation of the Septuagint into English will use the Septuagint as the base.) The MT contains עָלָיו-"upon it" for:
28:13 and the Lord stood at its top. He said, "I am the Lord, the God of your grandfather Abraham and the God of your father Isaac. I will give you and your descendants the ground you are lying on." [NET Bible]
The same preposition (עָלֶיהָ) is used later in the verse for "ground you are lying upon."
The spelling difference in the two is that the first ends with the suffix for third masculine plural ("him/it") while the second ends with the suffix for third feminine plural ("her/it").
What I can look at right now does not show if there is a marked textual variant on this verse.
Hebrew has no neutral gender. The same suffix would be used for either "over him [Jacob]" or "over it [the stairway]." And the NET dictionary notes that in a minority of cases עָל can be used for "next" or "against." Gesenius' Lexicon (skip over the Strong's at the top and go straight for the Lexicon) notes that it is a frequent preposition with a wide variety of meaning. These meanings fall within 4 classes.
- Upon in the physical sense (the most common)
- Being high over without touching
- The sense of neighborhood and contiguity.
- A sense of motion such as "He stretched his hand towards the waters."
It is the third sense that comes into play here. Gesenius notes that even this sense springs from and can be reduced to the sense of being over. It is used in Genesis 16:7 when Hagar is near a spring of water in the desert. Genesis 24:30 contains a double example of this sense:
Genesis 24:30 "And, look, he stood over the camels over the spring." [my translation]
We should imagine the scene as the servant is standing next to the camels which are lying down next to a spring of water. As the water is at ground level, anything on the ground would be over it. And for the servant to be over the camels (as the preposition primarily requires), they would have to be lying down. His head would be above theirs even though their feet are at the same level. This would also be the case with Genesis 28:13. Jacob is lying down and the Lord stands over him if the preposition is used that way. A case could be made for this as Jacob is lying down and Gesenius notes that this sense is most common with the receiver being at rest.
It's not a difference in source. It's a difference in how they understand the preposition 'al being used here.
To answer which is best, I would go with "over it [the stairway]" since the preposition is most commonly used for "over." I would also have a translation note like:
The Hebrew pronoun could refer to either Jacob or the stairway. Some translations render it such and take the preposition to mean that the Lord is standing next to but towering over Jacob.