I know it's been some time but I'm having hell of a release going on here. So I just didn't came to check on what's wrong with the saving of final transforms. I finally made it so that I'm not there 7am to 10pm every day. This means: it's fixing time.
To provide you with an acceptable solution, I just reverted the behavior of FXes to the one of 15C. So that you at least get to use 64 bit plugins / scripts AND final xforms
Here it is: [link]
It's a patch so just replace the EXE files in your installation. If you didn't update yet, you can with this. In this case, you also just replace the EXE files. Remember the release notes from the original 15D package, though. It contains valuable information on how to use 64 bit plugins and compile multi-architecture plugins (32/64) from existing and new plugin code.
See you soon