emerge of x3270 overwrites /usr/X11R6/lib/X11/fonts/misc/fonts.dir, with a fonts.dir that only includes the x3270 fonts. startx then fails, because X can't find its default 'fixed' font (which is invisible because it's no longer listed in fonts.dir). Workaround is to run mkfontdir on /usr/<...>/fonts/misc after emerging x3270.
While you are modifying the font issue, can you also look into why the make.conf optimizations aren't being sent to the compiler? I have a suspicion that the Imake system is overriding the user provided defaults, but I'm not sure.
Looks like seemant already fixed this.