[r0lZ]

Hum, sorry, but no. BD3D2MK3D is really a tool to convert 3D to MKV, and it has so many 3D-specific things that it is very difficult to change it to support 2D also. Furthermore, adding a 2D option will be confusing and complicated. And I'm not sure I want to create another, different tool to process the 2D movies only.

But you can easily encode and mux to MKV yourself. There is no need to create an intermediate ISO image. I use 2 different methods, depending of the structure of the movie I want to encode to MKV. The two methods require something to decrypt the original BD (like AnyDVD HD), MkvToolnix and a GUI to re-encode to h264 (like Lord Mulder's Simple x264 Launcher). You need a demuxer only for the second method.

If the movie is made of a single M2TS file (not nulti-angle with seamless branching), I do this:
1. - I open the M2TS in MkvToolnix GUI (or, if you prefer, in the older MkvMerge GUI), and I mux the streams I want to keep to a lossless MKV file. (You have to specify the languages of the audio and subtitle streams manually.)
2. - I open that lossless MKV file in the Simple x264 Launcher and I re-encode the video to h264. (I don't think it's possible if you want to encode to h265, but I have not verified.)
3. - I load the lossless MKV into MkvToolnix/MkvMerge GUI, and I replace the video stream with the re-encoded stream. (It is usually necessary to specify the frame rate, unless you have specified it to x264 in step 2). Then I remux the streams to the final MKV.
That's all folks!

If the movie is made of several M2TS files (multi-angle), there are 3 solutions. The simplest one is to simply encode each part independently (with points 1 and 2 above), then use MkvToolnix/MkvMerge GUI to join the part together and output the final MKV. However, that method is not perfect, because it introduces small delay problems at the joints. They are usually not perceptible if the movie has only 2 or 3 parts, but if it is made of numerous parts (like some Disney/Pixar movies) it's not recommended. In that case, I prefer to demux the MPLS file (you can use tsMuxeR or eac3to to do that, but eac3to is easier and it works well as long as the source is in 2D or if you don't need the subtitles). Then, you have to mux at least the video track to lossless MKV and encode it normally as explained above. Finally, you should mux the video, audio, subtitles and chapters to the final MKV file. There is also another solution for these difficult cases: use MakeMKV to generate the lossless MKV. It takes care of everything automatically, but it is not free and often it requires to analyse the movie during an extremely slow operation. (BTW, I have never understood why it's necessary. IMO, muxing directly with MkvMerge/MkvToolnix gives exactly the same result, as long as the original BD has been correctly decrypted.)

The method to process multi-angle movies is somewhat more tedious, but it works, and in both cases it's much more rapid than having to create an intermediate ISO. The key is that most builds of x264 can decode an existing MKV file to re-encode it. You cannot re-encode directly the M2TS because even if x264 accepts it, it doesn't decode it properly. It's why you have to do step 1 to convert the M2TS (or MPLS) to MKV first.

IMO, 3 manual steps to convert and re-encode a BD movie to MKV doesn't seem too complicated. Also, I suppose that there are other tools to re-encode a BD to MKV with x264 (although I don't know them because I have never needed them), and I don't want to reinvent the wheel.

To encode a 3D movie to 2D MKV, you can use BD3D2MK3D. When the project is ready, use _MUX_2D.cmd to mux to the lossless MKV automatically, and then follow points 2 and 3 above. I will add the possibility to re-encode automatically soon...