DVDs and BluRay discs are riddled with DRM. Some of those DRM solutions scramble up the content/structure of a DVD/BluRay disc pretty severely. The original disc will work in most hardware players, but it is not a given that software can unscramble the content. Most of the time it is best to use a tool that extracts all the content from a disc onto your hard drive. The extractor is more often than not capable of fixing whatever the DRM broke.
Then you use software like MakeMKV with the extracted content on your drive to create the final video file. Yes, that is time-consuming and requires a lot of free hard disk space every time you such a thing, but it is the most sure-fire way of getting a single video file from a bunch of .VOB files. Never had satisfying results with software that promises to do both those actions in one go.
From what you are writing here, you appear to have the same problem.
And please, look up the difference between a DVD and BluRay. Yes, both are using a plastic disc as a medium. And that is where all other similarities end. A BluRay disc can easily contain 10 times more data than a DVD can ever hope to manage. Which is why viewing and hearing a BluRay movie is many times better than any DVD.
Because of all that extra data, it will take a whole lot longer to extract content from a BluRay disc than from a DVD. Depending on the processing power of your computer, this difference can indeed be hours.
MKVToolnix is not really a tool for repairing broken .MKV files. It is great at editing such a video file (adding audio tracks or subtitles for example). The repair function in VLC is not too useful. Yes, it is able to repair a video file and it will let you view as much of the broken video file as it can. But it won't store those repairs, so the next time VLC opens the broken video file, VLC will need to go trough the whole repair cycle again.
With ripping discs, the result really depends on how proficient you and your tools are. The concept of "garbage in, garbage out" really applies. The most success I always had was doing each step separately, using tools that do one job and do that job well. The loss in time and the need for ample free storage space were (way back when) a price I was willing to pay for successful conversion.
Nowadays, I can't be .rsed to go through all of that crap again as video streaming sites and a good enough internet connection are too cheap and convenient.