trying to create a day night hyperlapse, but the drone does not use the exact same angles to take the photos (see the reference). Notice the alignment of the buildings. The drone is keeping alignment along the horizon, but not from left to right. Any thoughts or suggestions?

In which Hyperlapse mode are you shooting?
Make sure there is not much wind and the compass is properly calibrated.

Have you tried doing an align (some editors call it stabilise ) and then cropping?