I don't think that Bryan Singer would invalidate his own two movies in an attempt to reboot the franchise. "X3" sure because he didn't direct that film and probably the reason why he chose to ignore elements from that movie.
He chose to ignore elements from all
the previous films. First Class
is a reboot, according to the director. Also, according to Singer's public statements, he approved of Ratner's work on X3. The prerelease assumption that First Class
would only ignore X3 has not been borne out. The unlikely workarounds proposed to make FC fit the other films don't fit with the intent of FC.