I’ve no idea about using MobaXterm other than as an X11 server. As far as I can tell, it’s essentially a cygwin derivative, but its primary purpose (according to their own website) is to simplify access to remote systems – not development. This means compiling MRtrix3 on MobaXterm would probably require the same procedure as it might on Cygwin – at least that’s what it looks like from their limited documentation on the topic. I note it looks like the Qt packages are available on Cygwin, and since that’s the hardest dependency to get hold of, I reckon it should be possible to get it compiled. But you’d need to work out how to get packages Cygwin installed under MobaXterm.
More to the point, I doubt it would work particularly well, certainly the GUI aspects. These require OpenGL 3.3, and X11 servers tend not to support anything above OpenGL 2 – at least not for direct hardware-accelerated rendering. At best, you might get
mrview to work with software rendering, which isn’t something I’d particularly recommend given that the MSYS2 install gives you full performance already…
Also, while mobaxterm seems to offer lots of convenience functionality for accessing remote servers, I’m not sure what it offers as a terminal beyond what you can get with MSYS2 – other than tabs maybe?