When the website says "Join Multiple Factions" they probably forgot to add "All at the same time". Just remember the guilds in Skyrim and all the Beth babies complaining about quests closing off for helping rival factions....
It's frankly stupid how often the hero of Tamriel has been the archmage, the head of the dark brotherhood, the head of whatever the biggest mercenary group is, and the guildmaster of the thieves guild AT THE SAME TIME.
Not that I'm saying the game should make it absolutely impossible to do these things, but being in charge of one thing should make it more noticeably more difficult to be in charge of something else.
Hopefully Fallout 4 will just hold it to "this group really likes you" not "you are now the Provost of the Institute"