The Crystal Towers do not operate without the presence of Allags. For the 8th Umbral Calamity, the presence of G'raha Tia allowed Cid to do his research on the alternate timeline.

Without the presence of any Allags, the Crystal Towers become functionless for security reasons. To say the Allagan Empire does not exist, we need to remember that Amon's clone casted a powerful spell to stop the flow of time within the tower, lulling the surviving Allags and clones inside into a deep slumber.

Amon's clone put a part of the Allagan Empire to sleep inside the crystal tower during the Calamity of Earth (4th Umbral Calamity).

We only know of G'raha Tia, but there may be others inside the tower in a deep slumber.