הא רבי ישמעאל הא רבנן
This first baraita is in accordance with the opinion of Rabbi Yishmael, who derives that meat of a firstborn offering, which is an offering of lesser sanctity, cannot be consumed if the altar is damaged or absent, based upon the halakha pertaining to the blood of the firstborn. That second baraita is in accordance with the opinion of the Sages, who disagree with Rabbi Yishmael.
ואיבעית אימא הא והא בקדשי קדשים ומאי בשני מקומות קודם שיעמידו לוים את המשכן
And if you wish, say there is a different resolution of the two baraitot: Both this baraita and that baraita are referring to offerings of the most sacred order. And what does the second baraita mean when it says the food may be consumed in two locations? It is referring to when the Israelites arrive at a new camp, before the Levites erect the Tabernacle,