After the Shiloh Mishkan (Tabernacle) was destroyed during the war with the Pelishtim, the Aron (Ark) was taken. This was during the time of Eli HaKohen. After the Aron was taken back, the Mishkan was reestablished in the town of Nov, but it was eventually destroyed by Shaul HaMelech. The Mishkan was moved to Giv'on, where it remained until the Beit HaMikdash (Holy Temple) was eventually built by Shlomo HaMelech in Yerushalayim. It stayed in Nov for 13 years, and then it was moved to Giv'on for a period of 44 years. Then Shlomo HaMelech built the Beit HaMikdash.
The Mishnah says, “When the Mishkan was destroyed in Shiloh, and they came to Nov and then to Giv'on and established a Mishkan there, the Bamot (high places) became permitted once again.” We learn this from the Pasuk (verse) that talks about eventually entering Eretz Yisrael. It says, “For you will not have yet come to the resting place and to the inheritance.” What we’re implying here is that before we arrive at the resting place, and also before we arrive at the inheritance, Bamot are permitted. The resting place is the Mishkan at Shiloh, where it rested for a very long time. The Mishkan was in Shiloh for 369 years. So before that, the Bamot were allowed at Gilgal, before it got to Shiloh. The inheritance is the Beit HaMikdash that Shlomo HaMelech was eventually going to build. Before that are Nov and Giv'on, with 57 years total between them, when Bamot are going to be permitted as well. So therefore, at this point in time, the Bamot were permitted.
During this time period, Kodshei Kodashim (most holy offerings) could be eaten only within the curtains of the courtyard of the Mishkan they built. Kodshei Kalim, the lower level, could be eaten anywhere within the cities of Yisrael. They could be eaten anywhere. Bamot were permitted. A person could build the Bamah, a personal Mizbeach (altar), and do whatever he wanted to do. He could bring a Korban (offering), eat it, and that was anywhere. The same was true of Gilgal. The reason, though, is that when we’re talking about Gilgal, we use a different line. We say, Bekol Makom, it could be eaten anywhere. Over here, we say, Bekol Arei Yisrael, in any city of Yisrael. This is because the Jewish people had not yet settled. In the time of Gilgal, they only settled the land afterwards. After the full conquest of 14 years, they actually stayed in cities.