NO. that is wrong. The .prt is created in the BSP phase and used in the vis stage. If the map is leaked, it will not create one, but my suggestion was to see what is going on in the boxed map case to cause max visibility.
from tools/quake3/q3map2/bsp.c (which does the BSP pass)
/* save out information for visibility processing */
NumberClusters( tree );
if( !leaked )
WritePortalFile( tree );
-saveprt is set in the vis stage in case you want to keep it around after that, to look at it in the portal viewer. Otherwise, the vis stage deletes the .prt file, since there is no further need for it.