I've just installed Linux version 1.6.1 of MakeMKV, and I've tried ripping a couple of HD DVDs. Every time, the main title is split into two files. It seems that MakeMKV is unable to join the EVO-files if a title is split into more than file. I also tried this on the Blade Runner disc which uses seamless branching, and I got no option to rip any of the three movies, but all the different branches were available.
Here's an example (US release of Fletch)

When I tried the same disc on the Windows version of MakeMKV, it worked perfectly.
(One thing, though - when I say "disc", I really mean "folder structure, ripped by AnyDVDHD". I know AnyDVDHD doesn't always play nice with MakeMKV, but I'm guessing this isn't relevant in this case, since the same folder structure works in Windows)