The new eM Client 11 MSIX packages use system support for redirecting Simple MAPI calls into packaged applications. The relevant registry keys are these ones:
Neither HKLM\SOFTWARE\Clients\Mail\eM Client nor HKLM\SOFTWARE\WOW6432Node\Clients\Mail\eM Client is relevant anymore.
.mapimail is not in any way related and it’s not our registry keys.
I cannot really advise what to check next. The default value in HKEY_LOCAL_MACHINE\SOFTWARE\Clients\Mail should be PackagedMail. The default value in HKEY_CURRENT_USER\Software\Clients\Mail can be deleted, especially if it’s set to eM Client.