Welcome to the community @Ben_s! Thank you for sharing your solution.
At present, as you discovered, Keyman does not support non-US layouts well on Linux (or macOS). We have a tool called mcompile, which is a part of Keyman Desktop (for Windows) which rewrites a keyboard file to support non-US Latin script layouts such as German. It would be possible to use that program (I have no idea if it would run under Wine, sorry) to generate the German QWERTZ layout file and then manually copy that into your Linux installation.
You’d run it with something like the following command:
mcompile -d "C:\ProgramData\Keyman\Keyman Engine\Keyboard\_Package\sil_ipa\sil_ipa.kmx" kbdgr.dll 407 c:\temp\sil_ipa.kmx
Replace the final parameter with the output path for the transformed sil_ipa.kmx. Then copy that file over into your Linux Keyman keyboards path, replacing the existing sil_ipa.kmx.
You can omit the -d parameter if you wish to continue using deadkeys (-d means replace deadkeys with plain keys).