You can set general options for all compilations in /etc/makepkg.conf, and package specific options would probably be best handled by just downloading a PKGBUILD for the package in question and editing it to include the option you want to enable. makepkg won't ask you about options by default when building something, but it's not that complicated to edit the PKGBUILD prior to calling makepkg.
Is there anything akin to use flags ? Suppose there's a package you need to enable sonething not enabled by default, how painful is that ?
You can set general options for all compilations in /etc/makepkg.conf, and package specific options would probably be best handled by just downloading a PKGBUILD for the package in question and editing it to include the option you want to enable. makepkg won't ask you about options by default when building something, but it's not that complicated to edit the PKGBUILD prior to calling makepkg.