The Ciphers' knowledge of math and electronics makes them ideal replacements for the missing BoS Scribes. The BoS could send some troops to reinforce the defenses at Mesa Verde while the Ciphers can use their wizardry to repair the BoS's equipment. If the player has met both groups, he can suggest an alliance to the leaders. The good thing about the deal is that the Brotherhood won't have to deal with disgruntled Scribes; the bad thing is that all the repair work needs to be outsourced to the Ciphers and won't be done in-house.
There were two proposed Journal Entries. One would be the regular entry, and the other would be a "Dumb Journal Entry" presumably the one you'd see if you had low Intelligence. The entry also shows the different ways of finishing the quest.