The 2.95.3 cross toolchain has nothing to do with the original posters's problems, since libtool-native is a native package.
That aside, my statement that "OE puts all things it builds under $TMPDIR." is true since, as you correctly pointed out, OE doesn't build a 2.95.3 (yet). If it would, it would put it under $TMPDIR.
Anyway, the original poster has a problem with his native compiler, not with an OE built one. Aside from telling us more about your environment, what does config.log under $TMPDIR/work/libtool-native-.../ contain?