AnimeHat ..Since this is my first time doing one of these bear with me because I write ALOT x]
But don't worry , I think I've solved the first one at least
Here are my thoughts:
1) Because Link defeated/sealed Demise in the end of SS and placed the Master Sword into the pedestal, it probably means there were no more monsters or enemies left to bring havoc to temple. This idea is explained about twice in the game where you helped Batreaux the demon. When Batreaux became a human, monsters were no longer in Skyloft during the night times, and it is implied that dark aura brings about monsters. Fi also identifies Demise with a dark aura, and tells us he is the leader of the monsters existing at the time. (Now to get back to the topic) This means that when Demise was vanquished, there were no more of his servants to destroy the temple (as the Imprisoned tried to) so when Link placed the Master Sword into the pedestal, there was no one to lift the sword up and take it away. Technically, if you leave something secured int he past, it should appear in the future the way you left it. Kinda like a time capsule
Extra Bits: Two swords were probably not created at the same time, but the two swords (Master Sword and Goddess Sword) along with the Harps and all of the Hero's Gifts left behind by Hylia for A SHORT PERIOD OF TIME.
Idea: When Link went to the past at any time right after Hylia sealed Demise and gave up her Goddess-hood he carried the Hero's Gifts, The Goddess Harp, and the Hero's Gifts. At that point, Hylia's Goddess Sword and her Harp (perhaps along with Fi) and the Hero's Gifts that she was about to place away for Link to find in the future would have co-existed in the PAST when Link came to re-seal and defeat Demise. By that time the Goddess Sword would have been placed in the Goddess Statue along with Fi so that Link would use it as intended, which is what he did when he came to the PAST then put the sword back into the pedestal to return to his own time. However, when he returned to his own time, the Goddess Sword would not be in the Goddess Statues because the Master Sword IS the Goddess Sword in the point in time because he would have already used it to gain the Master Sword.
2) We have to look at the story through Link's eyes. The story begins with the entire story. Link defeats The Imprisoned several times and Zelda maintains that seal until Link can go into the PAST to go defeat Demise forever. After Demise is destroyed along with his Imprisoned form in the original time, it is true that the entire quest should not have happened as soon as Demise was defeated. But lets nto look at this with our logic. Lets look at this with the trends that run in the Zelda series.
We know that
1. Demise seems to have conquered time
2. Traveling in time creates a split-timeline scenario
Based on the fact that Demise seems to have conquered time, the idea of a time paradox like this could just be dismissed by using that excuse. Yeah, solving the paradox by using another paradox to explain the other, but since I don't have any ideas or theories to explain that, I'm just putting my 2 cents in there.
2) Time travel created quite a number of theory-solving in the Zelda series. Which is why I LOVE Zelda so much! Now, if your not familiar with Timelines beyond the Zelda franchise, then you might wanna hold on. Im not sure of your knowledge on the situation.
Think of the Skyward Sword story as a straight line. A VERY LONG ONE
<-(War Period)-(Hylia's Sealing of Demise)-(Skyloft Creation)--(Link's Quest)--(Zelda's Sealing)--(Zelda Recovered)--(Girahim to the Past)->
(correct me if I missed something)
Now at the last bit of the storyline Link must go back in time to seal Demise away. So from "(Girahim to the Past)" *No Pun Intended* Link needs to travel back to "(Hylia's Sealing of Demise)". After his destruction, when Link goes back to his own time it must have been as though NOTHING Link did would have ever happened because there was no need to vanquish a Demise that never existed in that point in time. But, why is everyone the way he left them? The only way for this to happen was that Link unknowingly created a news split-timeline.
-Skyloft Creation-Link's Quest-Zelda's Sealing-Zelda Recovered-Imprisoned Dead-Girahim to the Past-Demise's Defeat
(Hylia's Seal Demise)-/ ^
\(Skyloft Creation)--(Girahim Return's To Past)-(Link Defeating Them Both)-(Re-written Future)->
Now heres an over analyzation. Notice the straight arrow that links one split line to the other? I think thats when Link must've used the Gate of time to RETURN to that other timeline where everything was as it is. But at that point Link would have already gone through the gate to defeat Demise, so once he came back out it was concluded that he defeated Demise upon his return.
ONE LAST IDEA: I dont think it really made sense to go back in time to kill Demise. We already saw that Girahim going back in time created a Split, so he would not have been causing havoc in their time, but another. Demise also conquered time, but his grip on time must have been destroyed when the Imprisoned was crushed. When he was defeated in the future by the TRIFORCE, it was made certain in his own timeline that he existed that he would have had his days numbered from then on. He would only be able to live from the times he broke out as the Imprisoned onto the day when he got trampled on by The Goddess Statue.
(War Period)-(Demise vs Goddess Hylia)-(Sealing Away)-(Being Destroyed by the Triforce in one point in Time)->(Saved World Continues)->
\
\-(Girahim Returns)-(Link Defeats Them)--->(Saved World Continues)-->
That's why in my opinion, it didn't make sense to go back in time, you would not be saving yourself but another world at another time while your world was already saved because the Triforce defeated Demise already. I guess the only person left to defeat was Girahim. In other words, the whole thing (in my opinion) was about saving two timelines, that in the end had the exact same result, success!
So thats my thoughts lol..sorry for dragging it on! Tell me your thoughts if you're confused, tell me your opinion!
REMEMBER: THIS ENTIRE POST IS BASED ON MY THOUGHTS AND OPINION, I AM NOT CLAIMING THESE AS FACTS.