Hi Kilian,
The Atomic-ID header should work with either the full URI form of the transaction ID or just the UUID portion. We will need to update the documentation to indicate that the UUID is also acceptable.
I was not able to reproduce the issue you encountered, in testing I was able to provide the full URI form of the transaction ID as the Atomic-ID header. I tested using the fcrepo:6.0.0 docker container and the jetty console distribution. It may be that the Apache proxy you mentioned is affecting things, possibly by modifying the base URI in the header or some other arrangement. If fedora received a different base URI in the header then what is configured to be running on it would not be able to recognize the the Atomic-ID.