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The Gemora analyzes Rabbi Yishmael’s opinion: If he maintains that the initial sanctity of the Beis HaMikdash was sanctified for its time and for all future time, then it should even be permitted for a bechor to be brought as a sacrifice and be eaten in Yerushalayim? And if he holds that the initial sanctity of the Beis HaMikdash was sanctified for its time but not for all future time (and therefore nowadays there is no sanctity), then his inquiry (regarding ma’aser sheini) should have been relevant to a bechor as well (if a bechor was slaughtered while the Beis HaMikdash was in existence, and then it was destroyed, may it be eaten in Yerushalayim)? [Why was the halachah of bechor obvious to Rabbi Yishmael, but not the halachah regarding ma’aser sheini?]
Ravina answers: In truth, Rabbi Yishmael holds that the initial sanctity of the Beis HaMikdash was sanctified for its time but not for all future time, and here the reference is to the following case: The blood from a bechor was sprinkled before the destruction of the Beis HaMikdash, and then it was destroyed, and the meat was still present (and ready to be eaten). Rabbi Yishmael compares the meat of the bechor to its blood: when the blood may be sprinkled on the Altar, the meat may be eaten as well (but since now there is no Altar and the blood cannot be sprinkled, the meat may not be eaten either). And then he compares ma’aser sheini to bechor.
Tosfos (in Megillah 10a) cites the opinion of Rabbeinu Chaim that even if one maintains that the initial sanctification of the Beis HaMikdash was not for all time and it would be forbidden to offer sacrifices on the site of the Temple Altar, one is nonetheless prohibited from offering a sacrifice on a private altar.
Rashi disagrees and holds that if the sanctity of the Beis HaMikdash ceased by its destruction, it would be permitted to offer sacrifices on a private altar nowadays.
The commentators ask on Rabbeinu Chaim: If the sanctity ceased after the destruction, why would it be forbidden to offer sacrifices on a private altar? After the destruction of Shiloh, bamos became permitted, so why not after the destruction of the Beis HaMikdash?
Minchas Chinuch (254:7) writes that although Yerushalayim has lost its sanctity in regards to offering sacrifices and eating kodoshim, the city remains the “chosen place” and the third Beis HaMikdash will be built there. This is why private altars are still forbidden. This is the distinction between Shiloh and Yerushalayim. Shiloh was not the chosen city and when the Tabernacle was destroyed, there was no vestige of sanctity left in the city and bamos became permitted. Minchas Chinuch states that this is the explanation as to why we are still subject to a prohibition of fearing the Mikdash nowadays, since it is still the chosen place although it has not retained its sanctity.