It seems that flags defined in make.conf get stripped prior to Chromium compilation. Would it be possible to compile Chromium with LTO optimizations? If not, where is the barrier?
I can't see us adding an lto USE flag. You can use the custom-cflags USE flag to prevent the -flto flag from being dropped.
Also be aware that this need huge amounts of memory, e.g. you cannot build LTO chromium on a 8GB machine with gcc. Clang with -flto=thin is much better memory wise, but last time I've tried it crashed during the final link.
