I read he did face Mecca and did remove his shoes in both mosques. Granted, that was in the secular press.
Removing shoes in a mosque is traditional, just as covering the head in a synagogue. For mosques there’s actually a core practical reason - people don’t want to prostrate on floors that people have tracked mud on
Although I understand that the symbolism of “praying toward Mecca” might be alarming to a non-Muslim, it’s actually not “praying towards a Muslim symbol” but rather praying towards the Ka’aba. The Ka’aba (that black square building you see when TV news shows Mecca) contains an altar that according to Muslim tradition was built by Abraham. Muslims face the altar when they pray (regardless of where they are). The city of Mecca is not important - it’s the altar of Abraham.
So you could just as easily say the Pope faced the altar of Abraham when he prayed.
Actually, whether he was facing Jerusalem or facing Mecca, he was facing towards one of the symbols of one of the other great Abrahamic faiths (Judaism or Islam, respectively).