Though following that to the letter doesn't work, I was able to use it as a starting point and through trial and error, I was able to figure it out. Starting with disc 1 of Code Geass, there was an odd setup. The first 3 of 5 episodes were in their own separate files on the disc, but the only way to get episodes 4 and 5 were through the 1 big 2-hour file. So, getting that file out, I was able to use the ToolNix to split the file into the 5 episodes properly. One thing to note, is the screenshots on the webpage shown above are slightly out of date, as the wording on some drop-down menu items have changed. Here is what I did to get mine to work.
Since I knew the episodes were 24:07 long, and the file itself contained no additional junk (like ads or empty space), I was able to use that as a template for how the tool splits the files up. It is 99% perfect. The only flaw being, if the episodes aren't the EXACT same length, as in, even off by a fraction of a second, you'll have instances where the last few frames of an episode are seen in the first few frames of the next episodes file. Luckily for most if not all shows, those frames will be intro/outro material, and so it will be forgivable.
Also, remember how Handbrake was taking nearly 2 hours to complete 1 episode file? Using the ToolNix, on my 2 core processor, all 5 episodes were split and from what I can tell, came out lossless (since the output are still MKV files), and that process took exactly 1 minute and 20 seconds. So... VAST improvement! Now the only thing that could possibly hinder me, is if a disc has a file with episodes out of order, or if they share a file with an ad or anything which screws up the time intervals. But so far I haven't seen that, so, it's open season!
EDIT
After a little more trial and error, I figured out how to do it by chapter. So, if you use VLC Media Player, the time bar at the bottom of the video will show little dashes with each chapter. So if you can figure out how many chapters each episode contains, you can use the following options to make split go based on chapter. This was using that Trigun file from back when I first started, and the chapters are kinda random seeming.
So "before chapters" indicates where you want the cuts. So in the case of Trigun, starting with 6 means the first file will be chapters 1-6. Then 11 (note no spaces between numbers and commas) is episode 2, and so on. The final chapter of the disc is 35, so making the final number 31 means the final file in the process will start at 31 and go to the end. As you can see, Trigun (at least in my release I own) as an inconsistent number of chapters per episode. I imagine with most releases, this won't be the case. Especially newer releases with better made discs. But yes, that solves all of the problems I've encountered so far. Now episodes are coming out perfectly, and I just gotta get the nerve to go through my whole library, and hope I don't run out of HDD.