Hello,
Whether you work with MATISSE or BlueKenue or Janet or others, a mesh is based on a number of inputs from the user, such as boundary contours or surveyed lines or point. Therefore the mesh generator does not care what the projection is. It will create a mesh geometrically, based on a "length" or "density", which unit should be defined by the user in accordance with the user coordinate system.
For instance, if you load Lat-Long inputs, your edge length would have to be very very small, in the 10^-5 degrees. If you load mm inputs, your edge length might have to be very large in 10^+5 mm.
However, the TELEMAC system assumes distances dX,dY (,dZ) are referenced in metres (unless you work in spherical coordinates). Therefore UTM (Mercator) or Lambert (in France) are often the default coordinate system chosen by users, for the mesh, i.e. for the inputs used to build the mesh.
If you already have a mesh in a coordinate system that in not true to the distances in metres, you will have to convert your mesh into a more appropriate coordinate system. Blue Kenue can do such conversion for a number of coordinate systems. You can also program your own converter in python for instance, based on the existing tools available within pytel.
Hope this helps,
Sébastien.