You can use almost any projection you like when creating CartoType maps. The makemap data preparation tool accepts the same parameters as the PROJ.4 tool. Some examples:

Create a map of Indonesia using the Lambert azimuthal equal-area projection:

makemap +proj=laea +lat_0=-2 +lon_0=118 +ellps=WGS84 /graticule=1,15m /urbanareas=yes /extent=94,-12,142,8 /usgs=e:\new-height-data /input=e:\ctm1\coastlines.makemap indonesia.osm

Create a map of the world using the Azimuthal Equidistant projection (above), centered on London:

makemap +proj=aeqd +lat_0=51 +lon_0=0 +x_0=0 +y_0=0 +a=6371000 +b=6371000 +units=m +no_defs /merge=no /extent=-180,-90,180,90 world-base-map.xml world-base-map-low-res-azeqd.ctm1

The Spatial Reference web site is a good source of PROJ.4 parameters. Look up the projection by name, EPSG reference, etc., and click on the link named Proj4.