This makes software with strict Werror settings not fail on system includes. Example is devel/pructl which fails with -Werror -Weverything in histedit.h after adding USES=libedit.
/usr/local/include/histedit.h:41:9: error: macro name is a reserved identifier [-Werror,-Wreserved-id-macro] #define _HISTEDIT_H_ ^
and
/usr/local/include/histedit.h:191:14: error: padding struct 'struct HistEvent' with 4 bytes to align 'str' [-Werror,-Wpadded] const char *str; ^
Which is even more important, this flag should fix cases when a library is conflicting with it's own headers from the system. E.g. when libfoo is built and it has -I/usr/local/include -I. (in that order), it may pick up /usr/local/include/foo.h from it's previous version and break/miscompile. -isystem works in such a way than even if the same path is included with -I, it's still treated as system, regardless of argument ordering, so this is a reliable solution.