Nothing should have really changed MC wise for the workflow unless a bug was introduced.
Media Composer, like all other applications, have to use the RED SDK to decode R3D files. The difference is, all other applications give you full control over the RAW parameters, but MC is still only a subset. Other applications will let you trim R3D files as well.
I would see why decompose is not working – Typically its’ a decompose + handles and it should create new master clips which is what you would normally recapture with. Drop all those clips into a timeline, export CMX, back to Redcine (as you do) but consider a RED trim pass rather than making DNxHD. AMA those and relink giving you control over source parameters as well as resolution should you need to resize, etc.
Michael