The seal is on the tip of the brake line (inverted flare). There is a matching machined surface at the bottom of the threaded hole and that's where the seal is made (it's metal to metal, so don't use any Teflon tape or other type sealants).
So no, it does not necessarily need to thread to the same depth as the old (as referenced from the exterior). Just make sure it's tight, then after it's all together and you've bled the brakes, have your helper push hard on the brake pedal while you do a final leak test. Tim