I dare to post this answer, because the following tool is free and in my opinion everyone should know this great piece of software. Please forgive me! :-)
After some testing the best working solution I found so far can be archived by creating a heightmap in XNormals. Therefore I hope that you are on a windows system, because XNormals is a pure windows tool.
- Export your highpoly and your lowpoly and a cage as seperate Fbx scenes.
- Import them to XNormal (just drag the highpoly and the lowpoly into the list).
for the cage, a checkbox in the lowpoly object has to be enabled and you have to select it by clicking with RMB in the sceen and select "Browse external cage file"
- In the baking option select your texture size you want to export, your export location, and check heightmap as renderer.
- To render, press the Generate Maps button and after some calculating something like this should appear:
After adjusting your heightmap, close the window and it will export it to your predefined export location.