empty – indicates nothing specifically. Miqobot will travel through this waypoint in whatever state she was before (stealthed, mounted, or in flight).
beacon – a special type for Gathering. Shows Miqobot a possible spawn area of gathering nodes. Other than that, works completely like empty type.
Beacons are considered as “empty” waypoints, if you want to fly towards one while you started from a ground node, you need to create a flying waypoint between the ground one and the Beacon one.
What I usually do in this case, I enter in the Red Mode by pressing CTRL, and next to the Beacon, I left click on the lines that comes from ground waypoint and connect to the Beacon, and I add a Flying waypoint on each.
They will therefore remains straight lines and won’t change Miqobot path, just tell her to fly in order to reach the Beacon.
Maybe allowing to create a Flying Beacon type would help, but then again, this workaround is just a flew left clicks once you’re done with that part of the grid.
If you have to move the Beacon after you created the intermediate Flying waypoints, it will break your path with angles, just go back into the Red Mode, target those Flying waypoints and click on R to delete them one by one, you’ll end up again with straight lines, and then you can add them again by clicking on the lines next to the Beacon, roughly where you want them to be.