Man pages should probably go to $prefix/share/man rather than $prefix/man. The same is true for $prefix/texmfs which should probably go to $prefix/share/texmfs instead (I would probably pick something like $prefix/share/texmf-miktex).
(My package manager complains about the nonstandard locations.)
It would be even better if the location of texmfs (including its name) would be a parameter for cmake/ccmake rather than hardcoded.