I wasn't able to compile lyx-1.2.0.ebuild, until I changed the line 48: --with-extra-inc=/usr/X11R6/include/X11 ^^^ Nevertheless: good work!!
There is a new ebuild (lyx-1.2.0.2002075) that fixes this problem among others. Why aren't you using it? (emerge sync if you haven't in the last week or two). It's a known problem that the new ebuild fixed, so I'm closing this.