App-V 4.2 to App-V 4.6: Trouble brewing??

I am currently engaged in researching how .NET and Internet Explorer affect the process of sequencing applications under Microsoft's Virtualization technology App-V.
I recently posted about some of the underlying (even architectural) changes introduced with the Release of App-V 4.6. Especially, how it would affect .NET applications and whether or not including the required .NET dependency would adversely impact an existing 4.2 sequenced package when deployed under App-V 4.6 environments.
As part of this research on App-V application compatibility, I come across another little gem in the release notes found here: http://technet.microsoft.com/en-us/library/cc817171.aspx
It says,
"When upgrading 4.2 packages, you encounter problems caused by Windows Installer files in the Virtual File System
When upgrading a package from 4.2, you might experience issues relating to a mismatch of Windows Installer system files that were included by default in 4.2 and the Windows Installer libraries locally installed on your Sequencing workstation.
The following files are located in CSIDL_SYSTEM\:
• cabinet.dll
• msi.dll
• msiexec.exe
• msihnd.dll
• msimsg.dlll
And the proposed work-around is:
"Delete all of the preceding files from the package. Delete the mappings on the VFS tab as well as the actual files in the CSIDL_SYSTEM folder in your decode path."
Good advice. You need to get rid of these files from each an every sequenced package, in order to have full support for your App-V 4.6 deployments.
So, I decided to have a quick scan of some of our customers existing App-V sequenced packages (in the SFT file format) to determine how packages contained these files (and thus, would need updating, testing and redeployment.
Here is a quick snap-shot of the results from AOK tool.

I hid the name of the application package (SFT file) to protect the innocent.
Overall, for each application portfolio that I analysed the  results were roughly the same: approximately 60% of the scanned application packages (SFT) contained all of these files and would need to be updated, tested and redeployed .
Estimated 3-4 hours work for each application update, that translates to  roughly 4000 hours effort for one of our clients. Or,  two man years of effort.
And, I thought App-V was supposed to save you time and money....