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So to answer your question OP, you can join all 3 factions and the Institute and do all the quests and sidequests you want in any order except the quests that would force you to fight another faction (except fight agaisnt the Insittute obviously). If you don't actually care about the BOS, you can actually proceed to do a bunch of quests for the Institute and RR without worrying about anything until the point where their paths diverge.
You can refer to this chart to see which quest you will miss. The route that will allow you to complete the most mission would be to side with RR which would allow you to do all of RR's mission plus 90% of the Institute's missions and most of BOS' mission up until Tactical Thinking (and you could have done most if not all of their sidequests by this point).
http://cdn.gamerant.com/wp-content/uploads/fallout-4-mission-tree.png