One thing I thought of that I don't see covered is regarding the splitting of >4GB files.
Would it not be possible to split them at the end of the process rather than at the start?
This was a design decision. I had no end of problems with mp4box (the utility used by YAMB and XenonMKV) to split MP4 content after the fact, and if I figured if I was encountering issues with standard MKV files with AC3 audio, then there'd be no end of issues experienced by the public - who have literally thrown every imaginable type of MKV into this utility.

I would actually prefer to split content at the end, since a movie split is so disengaging, but I ran into issue after issue with the tools choking - even before I decided to write this utility.
I may try this style of split again in the future, but for now I'm going to leave it at "it wasn't working for me, so I didn't do it that way."
FWIW, I agree completely with Jake on this one.
I've had no end of problems splitting MP4s with mp4box, whether from the command-line or with YAMB, where the split worked just fine, but the "-001.mp4" file refused to play on the 360, while the "-002.mp4" played just fine.
MP4Box is doing something in the ISO header (i assume) that the 360 just doesn't like. XenonMKV splits the file as the first step, as noted in the OP's post, but sometimes the split is "awkward" in that it splits by size and continuity can definitely be lost.
Here, in a nutshell, is how I control splits to be a little less of a "train wreck" in continuity.
1. Load your MKV into your media player of choice. I personally use Media Player Classic. Note the total length of the video and seek to the "halfway" point in the video. So, assuming your video is one hour and thirty minutes, you'd manually "scan" to the 45 minute point in the video.
2. Now, play the video from the halfway point until you get to a scene change, or a point where a split wouldn't be so offending, say a long camera pullback. This is where you'd want to split the clip. Note the exact time in minutes, seconds and milliseconds. Write it down. Note: I find this MUCH easier to do with MPC since you can do a CTRL+G to see the exact timecode of your selected split point. Again, write down the timecode, including the milliseconds, such as 00:50:01.119. So in this example, I'm splitting the video at 50 minutes, 1 second and 119 milliseconds into the clip. This happens to be at the first scene change after the halfway point of a 1:38:35 movie I'm preparing.
3. Load the MKV into MKVMerge GUI, select the "Global" tab, check "Enable Splitting", check "...after this duration" and type in the exact time you noted in step 2. In my case, it's 00:50:01.119.
4. At the bottom of the MKVMerge GUI, modify the output filename from the default placed in the box. Normally, I simply add "-part1" to the filename. So if the GUI defaults to "path\Movie.mkv", modify it to "path\Movie-part1.mkv". Now, simply click the "Start Muxing" button and off you go. You'll be writing a new file, labelled "Movie-part1-001.mkv" to your destination folder. Once the "~001.mkv" file has been written and the GUI begins creating the "~002.mkv" file, click "Abort". At this point, you don't need the second file in the split, because...
5. Go BACK to the "Global" tab on MKVMerge GUI, click the "...after timecodes" button and in the requestor box next to it, type in the exact time you used in Step 3, MINUS 5 seconds!!! So in my Step 3 example, I would type in 00:49:56.119 as the split time. In the "Output Filename" box, change the "-part1" to "part2" and click "Start Muxing".
Let MKVMerge GUI complete the entire process of writing 2 files. You'll have "Movie-part2-001.mkv" and "Movie-part2-002.mkv". The first of these two clips will be the first half of your movie, split 5 seconds earlier than the split in Step 4 above, while the second of the two clips will be the second half of the movie, split 5 seconds earlier than the split point you chose for the first half "Movie-part1-001.mkv". Delete the "-part2-001.mkv" file, since it's essentially the same file as outputted in Step 4, albeit 5 seconds short at the end, while the "-part2-002.mkv" file is the entire second half of your movie PLUS 5 seconds of the end of the first half.
So essentially, you've split the movie at a scene change just over halfway through the entire clip, and created a second clip of the remaining half, but containing 5 seconds of the end of the first clip. The overlap helps maintain continuity, and splitting at scene changes helps prevent discontinuity.
Now, process both MKVs with XenonMKV's "Convert A Folder" option to process both files into XBox-ready MP4 files.
Agree with Jake that splitting is evil, but many times a necessary one, unless you re-render to WMV that doesn't require splitting. But OH that takes SO long to maintain HD properties.
