We also use FSLogix Office Container that's why I disabled all DEM settings for Office 365 except the "Shared Settings" and it works all like expected.

I think I use the default Import/Export settings:

[IncludeRegistryTrees]
HKCU\Software\Microsoft\Office\16.0\Common
HKCU\Software\Microsoft\Office\16.0\FirstRun
HKCU\Software\Microsoft\Office\16.0\Microsoft Office 2016
HKCU\Software\Microsoft\Office\16.0\Registration
HKCU\Software\Microsoft\Office\16.0\User Settings
HKCU\Software\Microsoft\Office\Common
HKCU\Software\Microsoft\Shared Tools\Proofing Tools
HKCU\Software\Microsoft\VBA

[IncludeFolderTrees]
<AppData>\Microsoft\AddIns
<AppData>\Microsoft\Bibliography
<AppData>\Microsoft\Office
<AppData>\Microsoft\Proof
<AppData>\Microsoft\Spelling
<AppData>\Microsoft\Templates
<AppData>\Microsoft\UProof
<LocalAppData>\Microsoft\Office\ONetConfig

[ExcludeFolderTrees]
<AppData>\Microsoft\Templates\LiveContent

AND some stuff to capture signatures in Outlook: (see: https://communities.vmware.com/t5/Dynamic-Environment-Manager/Outlook-for-FSLogix/ta-p/2852157)

[IncludeFolderTrees]
<AppData>\Microsoft\Signatures
<AppData>\Microsoft\Spelling
<AppData>\Microsoft\UProof

AND some stuff for OneDrive:

[IncludeRegistryTrees]
HKCU\Software\Microsoft\OneDrive

[IncludeFolderTrees]
<LocalAppData>\Microsoft\OneAuth