.Net 2.0 does not need to be installed to install the OWA extensions. Regarding your merge controls folder issue this is happening because we edit the controls folder in the exchweb directoryof the highest directory. We place our code in some of these files so we can show our icons.
So if you look at the highest numbered directory you should have a folder called controls originals copied by enterprise vault.
The following technote references a certain directory number but you may have a higher one. But the instructions will be the same:
If after following the technote above you still get the error then I would suggest opening a case with support as we would need to setup logging to have a look at what checksum comparisons are happenin g