Yes, tsMuxeR is a simple blu ray authoring program, so you won't have many choices on extras when trying to use it. One main movie mkv is all you'll be allowed to import when using ClownBD, as far as I am aware.
If you need a more complex movie structure, use MultiAVCHD, which can set up menus for you.
The ISO should hold all the video and audio. The MDS file can be used by ImgBurn to burn everything to a disk. I've never tried to use Winrar to examine an ISO file of a movie. But I quit using Winrar about six years ago too.
What size is the ISO file? Hover your cursor on it and see how big it is in gb. I normally play blu ray ISO files by mounting them in Slysoft's Virtual CloneDrive, then play with Arcsoft TMT 3 or the free player Media Player Classic HomeCinema.
Virtual CloneDrive is free to use: http://www.slysoft.com/en/virtual-clonedrive.html
You should test this ISO before burning anything. And I suggest getting a BD-RE disk while you are still experimenting. You'll need to format a BD-RE disk, but ImgBurn can do that...it'll take just as long to format as it will to do the actual burn.