So I asked the Railroad first to help me build the relay, thinking I was going to be able to ask for help from all three factions. I would've chosen the Minutemen had I known there was only one faction I could ask for help. My question is this: I haven't gone through the relay yet (in an hours-old save), but have built it with the Railroad's help. Can I reject their assistance and change who I want to help me? The answer is likely, "no," as I've already built the relay, but I'd really prefer the Minutemen over the Railroad as they are the most noble of the factions in my estimation.
Fallout 4 – The Molecular Level – Change Faction
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Best Answer
I can confirm what Unknown Zombie stated in his comment. It does not matter in terms of who you want to ally with for the end of the game.
I can confirm this because I chose the Brotherhood to assist me, and sided with the Institute to get their ending for my first playthrough. And did the opposite on my second playthrough. Neither side really so much as mentioned the fact that I chose their enemy to assist the relay build. It serves no function after that mission anyway.