I'm at a crossroads on what I want my character to achieve in the game and have a quick question that should be able to be answered without specific spoilers.

Does the main quest force a choice of factions to support or does that come through advancing faction quests?

Basically can I complete the main quest and then go back and choose a faction to take to the top of the commonwealth or do they all tie together?

You can follow each faction's main quest without worry of picking sides until the game blatantly tells you "Doing this action will cause {faction name} to become hostile." You can't miss it, at least form my experience.

However, at a certain point do they do all tie together and you will have to chose which faction(s) survive.