It appears that repoman does not complain about use flags containing periods. This should probably be added. 3.1.4 USE Flag Names A USE flag name may contain any of the characters [A-Za-z0-9+_@-]. It must begin with an alphanumeric character. Underscores should be considered reserved for USE_EXPAND, as described in section 11.1.1.
repoman support has been removed per bug 835013. Please file a new bug (or, I suppose, reopen this one) if you feel this check is still applicable to pkgcheck and doesn't already exist.