Yeah, it's most likely these "islands were ripped from the surface and are being held held by those "anchors" which are using the power of the Flagship to keep them floating

As for the destruction of The Cathedral; we found out that Late Allagan Empire (Clone Xande's time and roughly the time of Azys lla's sealing) stopped worshipping gods, atleast most of them. So it's destruction is probably showing their triumph and warning.

It would not surprise me if Clone Xande made worshipping gods illegal and proclaimed himself god-king.

Azys lla seems like it was a tourist attraction or at the very least allowed civilians to enter. Just like we can visit the white house and other gov't facilites perhaps the Allagans did the same?