Huge SS spoilers, I didn't want to cover, sorry for those lurking, or who haven't played it.
The ancient civilization was said in the SS prologue to be guarded and watched over-by Hylia, which makes sense as the people would have seen a time of prosperity which would lead to technological advancement as seen in SS, there doesn't seem to be a lot of room for a enemy to invade or attack "Hyrule" during a time of prosperity. Hyila is said to have been appointed by the Golden Goddesses, a short time after they created Hyrule, I don't think this game is going to take place in a void of nothingness. The only point in which this would make sense taking place prior to SS is during the battle with Demise, but that sets a precedent that the story won't exactly have Zelda in it as Hylia later became the first Zelda, and Hylia is the one leading that very fight against Demise.
None of this is to mention that SS specifically makes it a point to set-up characters like Demise, Impa, and yes Link, to establish origins. Demise is the parallel of Hyila, he is all that is evil and said to be the reason that the Chosen Hero and the current Zelda almost always face adversity. Link in SS, is directly hinted at and damn near described as being the very first hero. Now I know there's a quote in SS where Zelda says Hylia gave her chosen hero a sailcloth in the past and that's why the people of Skyloft hold that tradition, but you have to realize that the entirety of SS is based around the theoretical idea of a
Causality Loop, aka everything that happens feeds into itself to allow everything to happen. Hylia is Zelda, but Zelda doesn't realize this at the beginning of SS. Hylia does choose Link to save the world and be part of her plan. Link is a hero. Zelda does give Link a sailcloth. There are a minuscule amount of people in the past to carry the knowledge of Link and Zelda's actions on through word-of-mouth. Thus when Zelda says Hylia gave her chosen hero a sailcloth, she's unknowingly referring to herself and Link at that very moment. Also Impa, doesn't seem to know Link (or anyone who looks like him) prior to SS, and she dies at the end of SS, so it basically has to be a different Impa.
Finally the cover of this Famitsu, shows Link holding the Master Sword, the thing SS's story is based around the creation of. Thus by elimination if this were to take place prior to SS, this would then have to take place between the point in which Link leaves the complete Master Sword in the past, and the events of SS. Not only does this throw a huge monkey wrench in Hylia's plans throughout SS, there's absolutely no evidence to support the game taking place there. (man I love SS's Story, it's so good, unlike whatever the hell ALBW was smoking)
Yes, it is possible to just cop-out and ignore any connection to any other Zelda game and just say it takes place here or there, but at that point why even establish that it takes place to SS, and not just have it be it's own thing?
All in all, I severely doubt this is canon, but even if it is Skyloft's inclusion doesn't imply it has to be before SS, as Skyloft is still floating at the end of SS, and presumably the rest of the timeline. Finally finally
P), this is a crossover, that has already show to be pulling a lot of things from different Zelda games, it can still have it's own story but a doubt it will relate to the timeline or and other continuity in Zelda at all.
