As Chris mentions, drone footage can produce motion blur (or undesirable camera motion). First you will probably want to stabilize/smooth your footage.
Most likely markers are not needed for aerial footage and most of the 3D trackers will be able to handle basic moves.
Since this is your first 3D project, I would recommend relatively simple moves. You can run into issues with full 360 rotations, etc.
Lastly, the 3D camera solver module found in mocha AE v3 & mocha Pro v3 was designed as an alternative to feature based 3D trackers and excels on out of focus or blurred footage. It does not "replace" Syntheyes or PFtrack for feature depth, but may be an easier to learn workflow for newer users.
Best,
Ross