Either I'm not understanding what you are trying to do, or you are not understanding what makemkv does
When you open a BRD in makemkv it gives you a list of all the titles found on the disc. It does this by reading the index file that normally tells the BR player how to put the ts files together for each title. Each title can be one or more chapters. Normally the main feature is a single title made up up of many chapters. Its usually (thought not 100%) the single title with the largest file size and greatest number of chapters. The number of physical ts files that make up the title has nothing to do with the number of chapters, and can be one or many for a single title. Makemkv should automatically assemble all of the necessary ts files required to give you the complete title as a single mkv file.
What most of us do when ripping BRD is de-select the check boxes next to all of the titles except the main feature, then under the main feature decide which combination of audio and subtitle tracks you want to preserve. Then you will end up with a single mkv file for the entire movie. If you want to extract the bonus features (additional titles) you can, each of which will be extracted in its entirety into a separate mkv file. Make sure you are using the extract/convert to mkv option, not the disk copy/backup option when you run the rip. The latter would just give you all the raw files off the disk.
Does that make sense, or am I misunderstanding what you are trying to accomplish? I have never seen a BRD where the feature is split across more than one title, so I am not sure how you would end up with a feature split into more than one mkv file. Makemkv should behave basically the same whether its reading a BRD or DVD.
If you really do need to concatenate files for some reason, you might try MPEG Streamclip. I've never used it for mkv's, but used to use it alot for joining and editing mpeg2 encoded files from my DVR. Seems like it supports mp4 and mkv now.
Good luck!
Rob