The only way you could have 2 that were putting out the EXACT same wattage while one being louder would be to either have a different enclosure or a different woofer, or be in a different car.
If you had the EXACT same enclosure, amp with the exact same power being produced, same sub, in the exact same airspace, you would get the same SPL. EVERYTHING has to be the exact same.
Back to your question, if you had 2 putting out the exact same wattage but one was going to a 12" woofer and one was going to a 15" woofer, obviously one would be louder.
A watt is a watt, but better amplifiers, namely ones with better internals and better build quality might have less distortion and might be more efficient, also will probably last longer.