Why does Abe want to stop the originals from building the box?

In the causal trail, if the first set of Abe and Aaron don't create the time machine, that should ideally reset the timeline right to the beginning. There would never be a successful time machine created. Abe and Aaron would give up and move on to other projects. None of the skewed timelines would exist and none of the other Abes and Aarons would exist. Basically a complete reset, but guess Abe's not very successful.

Here's a Timeline wise explanation of the sequence of events in the movie, makes one appreciate the movie more.

Primer Timeline-wise Explanation

At the end of the film Abe considers both himself and Aaron to be hopelessly corrupted by what they have done. There is no trust between them and they cannot plausibly return to their previous lives. Abe wants a version of Aaron to continue being a husband, father and entrepeneur, for the sake of Aaron's family, and a version of himself to live the life he intended for himself.

The "corrupt" Abe intends to remain in the area, but essentially removing himself from society, for two purposes:

• To protect the "naive" Abe and Aaron and their families from the multiple "corrupt" Aarons that now exist.
• To prevent the "naive" Abe and Aaron from successfully using the boxes, through sabotage if necessary, until they give up and move on to another project. This serves both to protect them from the consequences of what they set out to do, but also to keep Aaron's family intact, because if they "get in the box", they're gone forever in that timeline.

(Aaron's cynical retort to Abe's intentions, that Abe should make copies of his wife and daughter to keep for himself, seems to confirm Abe's thinking that the "corrupted" Aaron will never have a healthy family life again.)

But to be clear, Abe's goal is not to return the world to a single Abe and a single Aaron. That is impossible now and he knows it. A box can only take him back to the point in time it was powered on. It cannot return him to a time before it was constructed, and it cannot alter their memories or "reset" the traveller in any physical sense.

As the film ends, the "naive" Abe has already constructed and powered on his failsafe box (that both "corrupt" Aaron and later Abe have exited from and then reset), and possibly the other two "normal use" boxes, but has never used them. The "naive" Aaron has not yet had the device's capabilities explained to him. The "corrupted" Abe used nitrous oxide to subdue his other while he was in bed sleeping, and tied him up in the closet for at least one entire day. It is possible the other Abe remembers some of this. The "corrupted" Aaron injected a drug into the milk carton to subdue his other without being seen, and tied him up in the attic.

And Abe knows, because Aaron told him, that Aaron found his secret "failsafe" box from the storage facility tenant list, and used it before Abe could, taking with him a second folded-up box. ("They are not one use only. They are reusable.") Then Aaron powered off Abe's failsafe, and once Aaron had powered on his own secure failsafe, he powered Abe's back on again.

So Abe is unable to go back far enough to power off all the boxes and prevent the "corrupted" Aaron from coming back; Abe would exit his "failsafe" box at a point just after the "corrupted" Aaron had already emerged. Aaron's box goes back further, so Aaron is in the dominant position. This is why Aaron taunts Abe in the airport scene, "I guess it [Abe's failsafe] just doesn't go back far enough."

Abe is unable to go back to a timeline that does not include the "corrupted" Aaron. All Abe can do is bluster and threaten Aaron, and try to protect his family, and their doubles, from Aaron's influence. The narration track is probably the third Aaron who overpowered his attacker and then left (or possibly even the "corrupted" Aaron) placing a phone call to the "naive" Aaron to clue him in on what has happened, as a way of apologizing for drugging him and putting him in the attic. "Corrupted" Abe's mission just got a lot harder...