Your findings are quite imprecise:
- Sabayon does clearly NOT put anything in /usr/portage.
- Maybe you found an ebuild for libusb in /usr/portage, where it is expected to be.
is Flashtool a precompiled binary? if so, it is compiled for x86 or x86_64 (i.e. 32bit or 64bit?). At any rate, libusb is 1.0.9, either a) wait for an upgrade from sabayon, b) install a new version of libusb with portage and the recompile any program linking to it [very not recommended] c) see if Flashtool relaly needs 1.0.14 or it was just compiled against it, in the latter case, see if you can find the sources and recompile Flashtool yourself against your current libusb.