Why not calling winetricks from appimage to install .Net runtimes then run your app after and also you can pack winetricks cache folder then copy back to home .cache to avoid downloading it with winetricks when first run.
You will also need to store winetricks on bin, download it from git simple search will show on google.
No need to store prefix to appimage OR you can if want to experiment more.
Anyways good luck.