All right. Being creative here and so far pretty much everything works. Here's the layout of things:
VMware Horizon View 5.2
ThinApp 4.7.3
Windows 7 x 64 inside View
Office 2010 natively installed, with some native applications that are plugins to office.
In order to get native plugins and virtualized plugins to work, I created thinapped entry points for the native office installation and added the optional appsync path to my addins. This works perfectly. I get both the native plugin and the virtualized ones, cohabiting harmoniously 
The issue:
Adobe Acrobat Pro integrates just as well as the rest of my other plugins, however it causes Office to do a self-repair everytime it starts.
It seems to be unable to read the following registry key and to load the MSCOMCTL.OCX file.
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Installer\UserData\S-1-5-18\Components\00965022248C1D110ADD000A9C502477
This key exists on the physical machine but isn't visible in the thinapped environment.
The Office 2010 Entry Points package is only the package.ini file, with 4 entry points defined as well as isolation modes set to merged for both the directoryisolationmode and the registryisolationmode.
Attempts at resolution:
- I added the following in my Acrobat package (HKEY_LOCAL_MACHINE.TXT) - didn't work.
isolation_merged HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Installer\UserData\S-1-5-18\Components\00965022248C1D110ADD000A9C502477
- I added the following in my Acrobat package (HKEY_LOCAL_MACHINE.TXT) - didn't work.
isolation_merged HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Installer\UserData\S-1-5-18
- I added the MSCOMCTL.OCX file to the Acrobat %systemsystem% folder - didn't work.
Any help would be appreciated!
Marc