I believe it's likely that that portal that Skull Kid, Link, and the Mask Salesman traveled through is the only portal between the two worlds, Hyrule and Termina, which I give reasons for here.

The Temple of Light is known to be in the exact center of the sacred realm ("The Temple of Light, situated in the very center of the Sacred Realm" ---Rauru) and the Temple of Time, being its counterpart, is in the same location in the Light World, just as Hera's Tower was for Ganon's Tower, etc., in ALTTP. This means that the Temple of Time is in the very center of Hyrule. In Twilight Princess, it's shown that the Temple of Time is in the Lost Woods. This is how its pedestal also appears in ALTTP. Since ALTTP occurs far later than TP (the timeline not mattering), it makes sense that the temple has decayed further, so that the pedestal appears outside as it does in TP, but the walls and columns have eroded completely away. The Lost Woods location is not surprising, since woods appear behind it in OoT, and the Lost Woods stretch all around the east of the map, linking Zora's River and Goron City to Kokiri Forest. So it's very easy to accept that these woods behind it could be the Lost Woods. Furthermore, Navi is last seen flying out the ToT window in the end of OoT. After the pre-emptive capture of Ganondorf spoken of by Aonuma, it would make sense that Link follow her trail, search for her where she went, out the window to the woods. This is indeed where we see him looking in the beginning of MM: in the Lost Woods. We don't know what exact point is the center of Hyrule or the Sacred Realm: it could be just outside the temple on its grounds, for instance, and I propose that the portal in the Lost Woods that Link fell through could be the very center of Hyrule, located in the Lost Woods just behind--- or under--- the Temple of Time.

Why is this a necessary argument? The only link between Hyrule and the Sacred Realm is known to be the Door of Time, which is located in the Temple of Time. This leads to the Chamber of Sages in the Temple of Light, the counterpart of the Master Sword chamber. The center of the worlds is where their only link is located. Now, if just outside the temple in the Lost Woods is the opening Skull Kid led Link through, with the chasm he fell through (containing the glowing masks) perhaps even being directly under the Master Sword Chamber, then this link would be in the very center of Hyrule as well. And where does it lead? To the Clock Tower, which as explained in the game is the exact center of Termina.

Since the central link between Hyrule and the Sacred Realm is the only passage between them, I think it's very likely that this central link between Hyrule and Termina is the only passage between them as well.

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