Yes.
If you look at each individual game and how the intertwine with the other games, they simply don't serve any significance. I'll give an example: Ocarina of Time is very important as it is the source of the time split. Skyward Sword is important as it presents the series' prequel leading to proceeding events. Let's use an example where you have a similar mini-series so to say, The Wind Waker. This title is important because it shows the resulting effect of Link not being present and Ganon forcing the Gods to flood Hyrule. Yet the FS games don't really have this sort of ultimate significance other than connecting to one another, in which case, they should be together separated from the other games.
Each title fits in with another game and explains something in order to connect to another a game (however weak or strong that connection may be), but the FS series doesn't. Minish Cap--the first game--is placed in a rather interesting spot yet it doesn't do anything to expand on the foundations SS left behind. It's sequel [Four Swords] does nothing to set up the next set of events that lead into OoT. Then you have the oddest of them all, Adventures. This game follows the exact same pattern as the previous two, in story, in charterers, in villains, in lore, yet is placed, what we can only assume, is several thousands years ahead and after TP. There's a large disconnect present now, where it feels as if the world of Hyrule moved on from all the Four Swords lore--the Hero of Men, the Four Sword, Link Force, Vaati--and on to the more traditional stuff with Ganondorf, the Triforce, the Master Sword etc. It completely disregards this and jumps straight back into that era as if the stuff in between in irrelevant. It's like as if you have Medieval period, the Industrial Revolution, and the modern era we currently live in, then in 500 or so years we go back into the Medieval era without literally no explanation.
I've provided arguments before supporting FSA placement, I'm not one of those Timeline haters, but is it the perfect scenario? No. Preferably, the Four Swords games would be all together and away from the other games. Whether that's on a completely separate timeline or just segregated is another question. This mini series has its own understanding of Hyrule lore and thus should all be one.