The Gutnick Chumash adds to the debate on this particular verse and recent Jerusalem archaeology brings a new perspective to consider.
The Chumash highlights the arguments by Mizrachi and Nachalas Ya'akov about Rashi's struggle with the grammar.
Mizrachi suggests Rashi was troubled why the verse states that a place was "prepared" without specifying for whom it was prepared. However, the basic understanding is that it was prepared for the Jewish people. Rashi was bothered by a logical problem: How could God tell the Jewish people that He had prepared a place when at that time the land was inhabited by enemies of the Jewish people? The word suggests the land was ready for habitation?
The Nachalas Ya'akov corrected the question, suggesting Mizrachi drifted, he put 'land' back in its'place'. Rashi was also troubled by the use of the word 'place' - This may be the root of Rashi's later difficulty when he described the land that folded under Jacob and the stariway that stretched from Beersheba through Jerusalem to Bethel. Due to the force of these questions, Rashi offered a second explanation that the preparation was in the spiritual realm. To reduce confusion among readers of his debate, Rashi says this is one of the verses which state that the heavenly Temple is aligned directly opposite its earthly counterpart. That the spiritual readiness opposite the place of the earthly Temple is not a new phenomenon. Rather it had already been prepared for many years as is evidenced by many verses including that Ya'akov slept at the site of the Temple at the beginning of Parshat Vayeitzei. Now God's plan was beginning to materialize.
(יא) וַיִּפְגַּ֨ע בַּמָּק֜וֹם וַיָּ֤לֶן שָׁם֙ כִּי־בָ֣א הַשֶּׁ֔מֶשׁ וַיִּקַּח֙ מֵאַבְנֵ֣י הַמָּק֔וֹם וַיָּ֖שֶׂם מְרַֽאֲשֹׁתָ֑יו וַיִּשְׁכַּ֖ב בַּמָּק֥וֹם הַהֽוּא׃
(11) He came upon a certain place and stopped there for the night, for the sun had set. Taking one of the stones of that place, he put it under his head and lay down in that place.
Beit El (makom) on Mount Moriah is potentially the place God had made ready and that Rashi was struggling with.
It seems more logical that the grammar would mutually refer a physical and a spiritual place and that Rashi limits it to spiritual because he has difficulty with the enemy inhabitants of the land.
Since the reference is past tense, as in God already prepared or made ready the place, naturally it would refer to a pre-existing place that God prepared for the Jewish people. Further, the spiritual Temple location on Mount Moriah appears quite specific, given its physical counterpart opposite it.
At this point I'm going to jump to the physical evidence of a pre-Torah Holy Temple that had already existed on Mount Moriah from the times of Shem-MalchiTzedek, to whom Abraham tithed and continued to operate until Jacob was exiled to Egypt. After Jacob, the evidence proves it went out of service and was not discovered again until King Hezekiah built defensive walls on the east side of the mountain. The constructors preserved the stone Temples main artifact, a stone pillar or matzevah, which Jacob set up, then they built the massive wall on and over the bedrock of the stone Temple site. In 2009 it was re-discovered in the City of David. The evidence is described in the video above. For more information.