Well, afaik, AnyDVD HD is not dead. It should be continued by
RedFox. (See
this.) Anyway, there are other ways to remove the protection from the original BD. You can now open MVC-MKV files created with MakeMKV (currently with some limitations, but the next version of MakeMKV should be better). And there are other BD decrypters around.
The philosophy of BD3D2MK3D is to re-encode the two views as SBS, T&B or Frame-Sequential. I don't think that adding the re-encoding in AVC+MVC is a job for BD3D2MK3D. And MakeMKV does already lossless AVC+MVC MKVs with the original BD files (without re-encoding). Doing the same thing with BD3D2MK3D will be more time consuming, because MkvMerge cannot accept MVC tracks. I will have to combine the MVC with the AVC track first, and that takes a long time and much disc space. However, I have considered to implement lossless remux of AVC+MVC to M2TS. tsMuxeR can mux the AVC and MVC tracks separately to M2TS. There are some limitations (no chapters and no metadata for example), but it's not fundamental. I'm still not sure I'll implement that, because I don't think that many peoples are interested in simply remuxing the original streams to create a huge M2TS file. Also, you can already do it with the tsMuxeR GUI. But I may do it when I'll have some free time, simply because it's easy. All I have to do is generate a cmd file and a meta file for tsMuxeR.
Anyway, BD3D2MK3D will never implement the decrypting operation itself, so merging the AVC+MVC tracks to MKV or M2TS will never be a solution to replace AnyDVD HD.