So what about the fact that Zelda tells Link to close the DoT?
The Door of Time and Master Sword also exist in the adult timeline where they need to find closure. I'm not saying that adult Link personally went to the ToT and put the sword back, but somehow it must've been done.
When young Link is sent back, we see that he never actually touched the Master Sword in this new timeline, so he couldn't literally lay it to rest - the MS has always rested in its pedestal here.
I do believe that the DoT closed after Link stepped out of the MS chamber. My conclusion: Approaching from the MS chamber, the DoT cannot remain shut, and approaching from the temple hall, the DoT cannot remain open (without the keys).
All of that means Zelda's words did not describe literal facts, yet they still don't contradict reality.
What about the matter with the Hylian Shield?
It's an item Link could carry as a child, so if he brings it back from the future, its place is taken by a child timeline equivalent (summoned from the bazaar). This works like time-travel in MM which I described earlier. In other words: gameplay mechanics.
And why have the ToC on Link's hand(and have Navi not be there) at all if they were trying to imply that this was the initial scene all over again?
You seem to misunderstand me, I don't say the courtyard scene is a flashback. Since I don't, your doubts should be self-explanatory:
We were shown that Navi left Link, so of course she cannot accompany him back to Zelda. I say "back" because, even though Link has never been to Zelda in this new timeline, he has been to her in the past of the adult timeline.
(One thing that some people don't realise is that the child and adult timelines in OoT are by no means split, they are one intact line, proven by its self-consistency regarding the Song of Storms and Nabooru's enslavement. The split only ever comes to pass by Zelda sending Link back the last time, which creates the all-new MM+TP timeline.)
As for Link having the Triforce, it's because Link (he as an entity, including his soul that travelled time) is still marked as the chosen one with the ToC crest. Therefore, he instantly receives his ToC in the new timeline, disrupting the Triforce and triggering the "divine prank" years later.
Your theory is pretty good, but I don't see how you could act like Zelda looking in a window somehow proves that the creators intended Link to have gone back to before he even met Zelda. Perhaps if you explain it in more detail I'd understand it better.
I'm certain that Zelda looking through the window means she's watching Ganondorf. Sure, it's all fine to say the gardens are her favourite place to be, but if so, she would just sit in the flower field instead of hanging around that window all day. She has zero reason to stare into the throne room (if she wants to see it she can just go in), unless something's going on where she cannot be present: Ganondorf's visit.
Arguing that Zelda's hobby is window-watching is just silly. It's one thing to say she is nosy, but another to say she enjoys wasting her time observing the throne room for no reason. And we cannot assume there is another important event for her to spy on when the only such event we were shown was Ganondorf's audience.
It's just totally implausible for Link to encounter Zelda in the exact same position when the circumstances are not also the same.
The developers didn't even think that deeply about it. They just took it for granted that the players would recognize that scene and the circumstances of back then as being the moment where Zelda spied on Ganondorf. How I know that? It's simply so obvious.
The times when I personally didn't find it so obvious yet, were times when I was desperately trying to prove a certain game placement, which naturally affects one's ability to look at things from the developer's eyes.
Oh yeah, and if you believe that Ganondorf never entered the SR what do you make of him seemingly imitating the Triforce when he speaks to Zant?
An homage to ALttP without the slightest storyline implications. Exactly like Ganondorf's final line, "blood-smeared history of light and darkness", which has been revealed to be an homage to "Hyrule's blood-smeared history of darkness" from OoT's Shadow Temple.