One problem with FOQA as currently set up is, as you note, that the OEM is very much out-of-the-loop. This can lead to some very strange conclusions by those reviewing the data for SYSTEMS problems, as often they have not much more to go on than the FCOM, which is not a detailed design decoument by any stretch of the imagination. (I've seen at least one formal presentation by an airline FOQA team of the "causes" of an incident which was clearly based on a very rudimentary understanding of the system design)
(By the same token, of course, the OEM is very much isolated from actual operational practices, so we can be pretty much at sea when trying to understand crew behaviour.)
The reality is that only a truly multidisciplinary "accident investigation" team can hope to understand a serious incident or accident in most cases. As a tool for monitoring adherence to SOPs and routine issues FOQA is a great idea. And as a tool to improve system reliability predictions and catch systems issues earlier it'd be great if the OEMs got something too. But neither operators nor OEMs should be in the accident investigation business, except to assist the REAL investigators.