Thanks for the inputs, for the time being I will try the manual patching.
According to the Board Integration page, Mender has been tested successfully with Thud. Does it mean that U-boot auto-patching is supposed to work with a certain U-boot version?
If so, could downgrading U-boot to a specific commit solve the issue? By looking at the meta-variscite-fslc layer’s repo, I can see that U-boot has been changed a lot of times, seemingly independently from the layer’s other developments.