Wait how exactly is the X3 connected in your system? Your initial post says you hooked it up straight to the amp. Your amp should have a gain knob instead of a separate box - if there is one that's usually because it's a mono amp for subwoofers so you can switch from normal music to Lil Jon without fumbling with the gain knob still on the amp out in the rack out back or the settings on the processor (which can do a -6dB to +6dB range on the preamp output for the subwoofer channels and the tweeter channels, allowing you to match them to the midwoofer).
Do you mean you hooked up the X3 to the amp of the stock entertainment system in the car inside the dash? If that's the case then the reason why it clips easily on Loudness War recordings is because these are low power, high gain/high input sensitivity amplifiers. That aux gain knob might not even be a gain knob, but it could either be a passive attenuator (ie for taming hot line signals) or an active "preamp" (primarily designed to compensate for weaker line sources), plus not having a lot of power (you'd be lucky to get a clean 25w per channel out of these).
Or are you using one of those discrete, lower power amps from Alpine or Focal? AFAIK the Alpines have a control unit (unless it's the one that hooks up to an Alpine HU) but IIRC the Focals don't. Is that what you have? Either way these should at least get you a clean 25w or more vs the stock audio system's amplifier.