Where is the Beit El of Yaacov’s dream - Jerusalem (Temple Mount) or the area where modern day Beit El is?

There are indeed a few locations mentioned in Rashi and it could be misleading. According to Rashi on Breshit 28:11, the place referred to where Yaacov prayed and then slept was the place of the Bet Hamikdash. However, Rashi on Pasuk 18, quotes R. Elazar who describes the the position of the ladder. The foot of the ladder was in Beer Sheva, its midsection hovered over the Bet Hamikdash, while its summit was over Bet El. The Ramban on Pasuk 17 says based upon the Gemara in Chullin 91b, that Yaaacov actually was in Bet El, but Hashem "brought" the mountain of the Bet Mikdash to Bet El. So it was like he was in two places at once. As far as the location of the historical Bet El it is near the present day Bet El.